1
|
Thi Hue Kien D, Edenborough K, da Silva Goncalves D, Thuy Vi T, Casagrande E, Thi Le Duyen H, Thi Long V, Thi Dui L, Thi Tuyet Nhu V, Thi Giang N, Thi Xuan Trang H, Lee E, Donovan-Banfield I, Thi Thuy Van H, Minh Nguyet N, Thanh Phong N, Van Vinh Chau N, Wills B, Yacoub S, Flores H, Simmons C. Genome evolution of dengue virus serotype 1 under selection by Wolbachia pipientis in Aedes aegypti mosquitoes. Virus Evol 2023; 9:vead016. [PMID: 37744653 PMCID: PMC10517695 DOI: 10.1093/ve/vead016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/26/2023] [Accepted: 03/03/2023] [Indexed: 09/26/2023] Open
Abstract
The introgression of antiviral strains of Wolbachia into Aedes aegypti mosquito populations is a public health intervention for the control of dengue. Plausibly, dengue virus (DENV) could evolve to bypass the antiviral effects of Wolbachia and undermine this approach. Here, we established a serial-passage system to investigate the evolution of DENV in Ae. aegypti mosquitoes infected with the wMel strain of Wolbachia. Using this system, we report on virus genetic outcomes after twenty passages of serotype 1 of DENV (DENV-1). An amino acid substitution, E203K, in the DENV-1 envelope protein was more frequently detected in the consensus sequence of virus populations passaged in wMel-infected Ae. aegypti than wild-type counterparts. Positive selection at residue 203 was reproducible; it occurred in passaged virus populations from independent DENV-1-infected patients and also in a second, independent experimental system. In wild-type mosquitoes and human cells, the 203K variant was rapidly replaced by the progenitor sequence. These findings provide proof of concept that wMel-associated selection of virus populations can occur in experimental conditions. Field-based studies are needed to explore whether wMel imparts selective pressure on DENV evolution in locations where wMel is established.
Collapse
Affiliation(s)
| | - Kathryn Edenborough
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Daniela da Silva Goncalves
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - Tran Thuy Vi
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Etiene Casagrande
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Huynh Thi Le Duyen
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Vo Thi Long
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Le Thi Dui
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Vu Thi Tuyet Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Giang
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Huynh Thi Xuan Trang
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Elvina Lee
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - I’ah Donovan-Banfield
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - Huynh Thi Thuy Van
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | | | - Nguyen Thanh Phong
- Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
| | - Bridget Wills
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Heather Flores
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Cameron Simmons
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| |
Collapse
|
2
|
Malinova I, Zupok A, Massouh A, Schöttler MA, Meyer EH, Yaneva-Roder L, Szymanski W, Rößner M, Ruf S, Bock R, Greiner S. Correction of frameshift mutations in the atpB gene by translational recoding in chloroplasts of Oenothera and tobacco. THE PLANT CELL 2021; 33:1682-1705. [PMID: 33561268 PMCID: PMC8254509 DOI: 10.1093/plcell/koab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/02/2021] [Indexed: 05/10/2023]
Abstract
Translational recoding, also known as ribosomal frameshifting, is a process that causes ribosome slippage along the messenger RNA, thereby changing the amino acid sequence of the synthesized protein. Whether the chloroplast employs recoding is unknown. I-iota, a plastome mutant of Oenothera (evening primrose), carries a single adenine insertion in an oligoA stretch [11A] of the atpB coding region (encoding the β-subunit of the ATP synthase). The mutation is expected to cause synthesis of a truncated, nonfunctional protein. We report that a full-length AtpB protein is detectable in I-iota leaves, suggesting operation of a recoding mechanism. To characterize the phenomenon, we generated transplastomic tobacco lines in which the atpB reading frame was altered by insertions or deletions in the oligoA motif. We observed that insertion of two adenines was more efficiently corrected than insertion of a single adenine, or deletion of one or two adenines. We further show that homopolymeric composition of the oligoA stretch is essential for recoding, as an additional replacement of AAA lysine codon by AAG resulted in an albino phenotype. Our work provides evidence for the operation of translational recoding in chloroplasts. Recoding enables correction of frameshift mutations and can restore photoautotrophic growth in the presence of a mutation that otherwise would be lethal.
Collapse
Affiliation(s)
- Irina Malinova
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Arkadiusz Zupok
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Amid Massouh
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Etienne H Meyer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Witold Szymanski
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Margit Rößner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| |
Collapse
|
3
|
Yu C, Miao R, Ye Z, MacFarlane S, Lu Y, Li J, Yang J, Yan F, Dai L, Chen J. Integrated Proteomics and Transcriptomics Analyses Reveal the Transcriptional Slippage of P3N-PIPO in a Bymovirus. Viruses 2021; 13:1247. [PMID: 34206959 PMCID: PMC8310318 DOI: 10.3390/v13071247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
P3N-PIPO (P3 N-terminal fused with Pretty Interesting Potyviridae ORF), the movement protein of potyviruses, is expressed as a translational fusion with the N-terminus of P3 in potyviruses. As reported in previous studies, P3N-PIPO is expressed via transcriptional slippage at a conserved G2A6 slippery site in the genus Potyvirus. However, it is still unknown whether a similar expression mechanism of P3N-PIPO is used in the other genera of the family Potyviridae. Moreover, due to the extremely low expression level of P3N-PIPO in natural virus-infected plants, the peptides spanning the slippery site which provide direct evidence of the slippage at the protein level, have not been identified yet. In this study, a potato virus X (PVX)-based expression vector was utilized to investigate the expression mechanism of P3N-PIPO. A high expression level of the P3N-PIPO(WT) of turnip mosaic virus (TuMV, genus Potyvirus) was observed based on the PVX expression vector. For the first time, we successfully identified the peptides of P3N-PIPO spanning the slippery site by mass spectrometry. Likewise, the P3N-PIPO(WT) of wheat yellow mosaic virus (WYMV, genus Bymovirus) was also successfully expressed using the PVX expression vector. Integrated proteome and transcriptome analyses revealed that WYMV P3N-PIPO was expressed at the conserved G2A6 site through transcriptional slippage. Moreover, as revealed by mutagenesis analysis, Hexa-adenosine of the G2A6 site was important for the frameshift expression of P3N-PIPO in WYMV. According to our results, the PVX-based expression vector might be used as an excellent tool to study the expression mechanism of P3N-PIPO in Potyviridae. To the best of our knowledge, this is the first experimental evidence for the expression mechanism of P3N-PIPO in the genus Bymovirus, the only genus comprising bipartite virus species in the family Potyviridae.
Collapse
Affiliation(s)
- Chulang Yu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Runpu Miao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Zhuangxin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Stuart MacFarlane
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Junmin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China;
| | - Jianping Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| |
Collapse
|
4
|
Unconventional viral gene expression mechanisms as therapeutic targets. Nature 2021; 593:362-371. [PMID: 34012080 DOI: 10.1038/s41586-021-03511-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Unlike the human genome that comprises mostly noncoding and regulatory sequences, viruses have evolved under the constraints of maintaining a small genome size while expanding the efficiency of their coding and regulatory sequences. As a result, viruses use strategies of transcription and translation in which one or more of the steps in the conventional gene-protein production line are altered. These alternative strategies of viral gene expression (also known as gene recoding) can be uniquely brought about by dedicated viral enzymes or by co-opting host factors (known as host dependencies). Targeting these unique enzymatic activities and host factors exposes vulnerabilities of a virus and provides a paradigm for the design of novel antiviral therapies. In this Review, we describe the types and mechanisms of unconventional gene and protein expression in viruses, and provide a perspective on how future basic mechanistic work could inform translational efforts that are aimed at viral eradication.
Collapse
|
5
|
Immunohistochemical detection of the pro-apoptotic Bax∆2 protein in human tissues. Histochem Cell Biol 2020; 154:41-53. [PMID: 32200452 DOI: 10.1007/s00418-020-01874-w] [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] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
The pro-apoptotic Bax isoform Bax∆2 was originally discovered in cancer patients with a microsatellite guanine deletion (G8 to G7). This deletion leads to an early stop codon; however, when combined with the alternative splicing of exon 2, the reading frame is restored allowing production of a full-length protein (Bax∆2). Unlike the parental Baxα, Bax∆2 triggers apoptosis through a non-mitochondrial pathway and the expression in human tissues was unknown. Here, we analyzed over 1000 tissue microarray samples from 13 different organs using immunohistochemistry. Bax∆2-positive cells were detected in all examined organs at low rates (1-5%) and mainly scattered throughout the connective tissues. Surprisingly, over 70% of normal colon samples scored high for BaxΔ2-positive staining. Only 7% of malignant colon samples scored high, with most high-grade tumors being negative. A similar pattern was observed in most organs examined. We also showed that both Baxα and Bax∆2 can co-exist in the same cells. Genotyping showed that the majority of Bax∆2-positive normal tissues contain no G7 mutation, but an unexpected high rate of G9 was observed. Although the underlying mechanism remains to be explored, the inverse correlation of Bax∆2 expression with tissue malignancy suggests that it may have a clinical implication in cancer development and treatment.
Collapse
|
6
|
Zhao SN, Liu LL, Lv ZP, Wang XH, Wang CH. Network analysis of HBV‑ and HCV‑induced hepatocellular carcinoma based on Random Forest and Monte Carlo cross‑validation. Mol Med Rep 2017; 16:2411-2416. [PMID: 28656273 DOI: 10.3892/mmr.2017.6861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 03/28/2017] [Indexed: 11/06/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer‑associated mortality worldwide. Hepatitis B virus (HBV) and hepatitis C virus (HCV) are two common risk factors for HCC. The majority of patients with HCC present at an advanced stage and are refractory to therapy. It is important to identify a method for efficient diagnosis at early stage. In the present study gene expression profile data, generated from microarray data, were pretreated according to the annotation files. The genes were mapped to pathways of Ingenuity Pathways Analysis. Dysregulated pathways and dysregulated pathway pairs were identified and constructed into individual networks, and a main network was constructed from individual networks with several edges. Random Forest (RF) classification was introduced to calculate the area under the curve (AUC) value of this network. Subsequently, 50 runs of Monte Carlo cross‑validation were used to screen the optimal main network. The results indicated that a total of 4,929 genes were identified in the pathways and gene expression profile. By combining dysregulated pathways with Z<0.05 and dysregulated pathway pairs with Z<0.2, individual networks were constructed. The optimal main network with the highest AUC value was identified. In the HCV group, the network was identified with an AUC value of 0.98, including 41 pairs of pathways, and in the HBV group, the network was identified with an AUC value of 0.94, including eight pairs of pathways. In addition, four pairs were identified in both groups. In conclusion, the optimal networks of HCV and HBV groups were identified with the highest AUC values. The use of these networks is expected to assist in diagnosing patients effectively at an early stage.
Collapse
Affiliation(s)
- Shan-Na Zhao
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| | - Ling-Ling Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated Shandong University, Jinan, Shandong 250021, P.R. China
| | - Zhi-Ping Lv
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| | - Xiao-Hua Wang
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| | - Cheng-Hong Wang
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| |
Collapse
|
7
|
Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin. mBio 2017; 8:mBio.02298-16. [PMID: 28196963 PMCID: PMC5312086 DOI: 10.1128/mbio.02298-16] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes. Influenza A viruses are divided into subtypes based on the antigenicity of the viral surface glycoproteins hemagglutinin (HA) and neuraminidase. Of the 16 HA subtypes (H1 to -16) maintained in waterfowl reservoirs of influenza A viruses, H5 and H7 viruses often become highly pathogenic through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been known since the 1980s, the genetic basis for nucleotide insertions has remained unclear. This study shows the potential role of the viral RNA secondary structure for nucleotide insertions and demonstrates a key mechanism explaining why the acquisition of the polybasic HA cleavage site is restricted to particular HA subtypes in nature. Our findings will contribute to better understanding of the ecology of influenza A viruses and will also be useful for the development of genetically modified vaccines against H5 and H7 influenza A viruses with increased stability.
Collapse
|
8
|
Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
Collapse
Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| |
Collapse
|
9
|
Hagiwara-Komoda Y, Choi SH, Sato M, Atsumi G, Abe J, Fukuda J, Honjo MN, Nagano AJ, Komoda K, Nakahara KS, Uyeda I, Naito S. Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses. Sci Rep 2016; 6:21411. [PMID: 26898356 PMCID: PMC4761962 DOI: 10.1038/srep21411] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/22/2016] [Indexed: 01/09/2023] Open
Abstract
RNA viruses use various strategies to condense their genetic information into small genomes. Potyviruses not only use the polyprotein strategy, but also embed an open reading frame, pipo, in the P3 cistron in the -1 reading frame. PIPO is expressed as a fusion protein with the N-terminal half of P3 (P3N-PIPO) via transcriptional slippage of viral RNA-dependent RNA polymerase (RdRp). We herein show that clover yellow vein virus (ClYVV) produces a previously unidentified factor, P3N-ALT, in the +1 reading frame via transcriptional slippage at a conserved G(1-2)A(6-7) motif, as is the case for P3N-PIPO. The translation of P3N-ALT terminates soon, and it is considered to be a C-terminal truncated form of P3. In planta experiments indicate that P3N-ALT functions in cell-to-cell movement along with P3N-PIPO. Hence, all three reading frames are used to produce functional proteins. Deep sequencing of ClYVV RNA from infected plants endorses the slippage by viral RdRp. Our findings unveil a virus strategy that optimizes the coding capacity.
Collapse
Affiliation(s)
| | - Sun Hee Choi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masanao Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Go Atsumi
- Iwate Biotechnology Research Center, Kitakami 024-0003, Japan
- National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan
| | - Junya Abe
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Junya Fukuda
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Atsushi J. Nagano
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi 332-0012, Japan
- Faculty of Agriculture, Ryukoku University, Otsu 520-2194, Japan
| | - Keisuke Komoda
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenji S. Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Ichiro Uyeda
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Satoshi Naito
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| |
Collapse
|
10
|
Olspert A, Chung BYW, Atkins JF, Carr JP, Firth AE. Transcriptional slippage in the positive-sense RNA virus family Potyviridae. EMBO Rep 2015; 16:995-1004. [PMID: 26113364 PMCID: PMC4552492 DOI: 10.15252/embr.201540509] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 11/15/2022] Open
Abstract
The family Potyviridae encompasses ~30% of plant viruses and is responsible for significant economic losses worldwide. Recently, a small overlapping coding sequence, termed pipo, was found to be conserved in the genomes of all potyvirids. PIPO is expressed as part of a frameshift protein, P3N-PIPO, which is essential for virus cell-to-cell movement. However, the frameshift expression mechanism has hitherto remained unknown. Here, we demonstrate that transcriptional slippage, specific to the viral RNA polymerase, results in a population of transcripts with an additional "A" inserted within a highly conserved GAAAAAA sequence, thus enabling expression of P3N-PIPO. The slippage efficiency is ~2% in Turnip mosaic virus and slippage is inhibited by mutations in the GAAAAAA sequence. While utilization of transcriptional slippage is well known in negative-sense RNA viruses such as Ebola, mumps and measles, to our knowledge this is the first report of its widespread utilization for gene expression in positive-sense RNA viruses.
Collapse
Affiliation(s)
- Allan Olspert
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - John F Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| |
Collapse
|
11
|
Abstract
Plant viruses that contain plus-sensed single-stranded RNA genomes are highly abundant in nature. As the equivalents of large mRNAs, these viral genomes utilize a wide variety of gene expression strategies for the production of their encoded proteins. The potyviruses, which are among the most agriculturally important members in this category, contain a single large open reading frame (ORF) coding for a polyprotein that is processed into functional units. For many years, the products derived from the full-length polyprotein were thought to be the only functional viral proteins. However, this notion was dispelled when an additional essential viral ORF, PIPO, was discovered encoded in an alternative reading frame. Since then, the PIPO protein—P3N-PIPO, which mediates virus movement in plants—has been intensively studied, but its mode of expression remained elusive until now. Two articles, one in this issue of EMBO Reports , now report that slippage of the viral polymerase during viral genome replication is responsible for shifting PIPO into a translated reading frame, thereby allowing for production of P3N-PIPO 1 ,2 . This mechanism of gene expression represents a novel strategy for plant viruses.
Collapse
Affiliation(s)
- K Andrew White
- Department of Biology, York UniversityToronto, ON, Canada
| |
Collapse
|
12
|
Rodamilans B, Valli A, Mingot A, San León D, Baulcombe D, López-Moya JJ, García JA. RNA polymerase slippage as a mechanism for the production of frameshift gene products in plant viruses of the potyviridae family. J Virol 2015; 89:6965-7. [PMID: 25878117 PMCID: PMC4468506 DOI: 10.1128/jvi.00337-15] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Adrian Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ares Mingot
- Center for Research in Agricultural Genomics CRAG, CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - David San León
- Centro Nacional de Biotecnología CNB, CSIC, Madrid, Spain
| | - David Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Juan J López-Moya
- Center for Research in Agricultural Genomics CRAG, CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Juan A García
- Centro Nacional de Biotecnología CNB, CSIC, Madrid, Spain
| |
Collapse
|
13
|
Koutmou KS, Schuller AP, Brunelle JL, Radhakrishnan A, Djuranovic S, Green R. Ribosomes slide on lysine-encoding homopolymeric A stretches. eLife 2015; 4:e05534. [PMID: 25695637 PMCID: PMC4363877 DOI: 10.7554/elife.05534] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 02/18/2015] [Indexed: 01/29/2023] Open
Abstract
Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of synonymous AAG codons. Kinetic studies in E. coli reveal that differential protein production results from pausing on consecutive AAA-lysines followed by ribosome sliding on homopolymeric A sequence. Translation in a cell-free expression system demonstrates that diminished output from AAA-codon-containing reporters results from premature translation termination on out of frame stop codons following ribosome sliding. In eukaryotes, these premature termination events target the mRNAs for Nonsense-Mediated-Decay (NMD). The finding that ribosomes slide on homopolymeric A sequences explains bioinformatic analyses indicating that consecutive AAA codons are under-represented in gene-coding sequences. Ribosome 'sliding' represents an unexpected type of ribosome movement possible during translation.
Collapse
Affiliation(s)
- Kristin S Koutmou
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
| | - Anthony P Schuller
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
| | - Julie L Brunelle
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, United States
| | - Aditya Radhakrishnan
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, United States
| |
Collapse
|
14
|
Expression of the novel hepatitis C virus core+1/ARF protein in the context of JFH1-based replicons. J Virol 2015; 89:5164-70. [PMID: 25694591 DOI: 10.1128/jvi.02351-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 02/09/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus contains a second open reading frame within the core gene, designated core+1/ARF. Here we demonstrate for the first time expression of core+1/ARF protein in the context of a bicistronic JFH1-based replicon and report the production of two isoforms, core+1/L (long) and core+1/S (short), with different kinetics.
Collapse
|
15
|
Zhou YN, Lubkowska L, Hui M, Court C, Chen S, Court DL, Strathern J, Jin DJ, Kashlev M. Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli. J Biol Chem 2013; 288:2700-10. [PMID: 23223236 PMCID: PMC3554936 DOI: 10.1074/jbc.m112.429464] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 01/05/2023] Open
Abstract
Transcription fidelity is critical for maintaining the accurate flow of genetic information. The study of transcription fidelity has been limited because the intrinsic error rate of transcription is obscured by the higher error rate of translation, making identification of phenotypes associated with transcription infidelity challenging. Slippage of elongating RNA polymerase (RNAP) on homopolymeric A/T tracts in DNA represents a special type of transcription error leading to disruption of open reading frames in Escherichia coli mRNA. However, the regions in RNAP involved in elongation slippage and its molecular mechanism are unknown. We constructed an A/T tract that is out of frame relative to a downstream lacZ gene on the chromosome to examine transcriptional slippage during elongation. Further, we developed a genetic system that enabled us for the first time to isolate and characterize E. coli RNAP mutants with altered transcriptional slippage in vivo. We identified several amino acid residues in the β subunit of RNAP that affect slippage in vivo and in vitro. Interestingly, these highly clustered residues are located near the RNA strand of the RNA-DNA hybrid in the elongation complex. Our E. coli study complements an accompanying study of slippage by yeast RNAP II and provides the basis for future studies on the mechanism of transcription fidelity.
Collapse
Affiliation(s)
- Yan Ning Zhou
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Lucyna Lubkowska
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Monica Hui
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Carolyn Court
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Shuo Chen
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Donald L. Court
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Jeffrey Strathern
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Ding Jun Jin
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Mikhail Kashlev
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| |
Collapse
|
16
|
Strathern J, Malagon F, Irvin J, Gotte D, Shafer B, Kireeva M, Lubkowska L, Jin DJ, Kashlev M. The fidelity of transcription: RPB1 (RPO21) mutations that increase transcriptional slippage in S. cerevisiae. J Biol Chem 2012; 288:2689-99. [PMID: 23223234 DOI: 10.1074/jbc.m112.429506] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The fidelity of RNA synthesis depends on both accurate template-mediated nucleotide selection and proper maintenance of register between template and RNA. Loss of register, or transcriptional slippage, is particularly likely on homopolymeric runs in the template. Transcriptional slippage can alter the coding capacity of mRNAs and is used as a regulatory mechanism. Here we describe mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II that substantially increase the level of transcriptional slippage. Alleles of RPB1 (RPO21) with elevated slippage rates were identified among 6-azauracil-sensitive mutants and were also isolated using a slippage-dependent reporter gene. Biochemical characterization of polymerase II isolated from these mutants confirms elevated levels of transcriptional slippage.
Collapse
Affiliation(s)
- Jeffrey Strathern
- National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Hepatitis C viral protein translation occurs in a cap-independent manner through the use of an internal ribosomal entry site (IRES) present within the viral 5'-untranslated region. The IRES is composed of highly conserved structural domains that directly recruit the 40S ribosomal subunit to the viral genomic RNA. This frees the virus from relying on a large number of translation initiation factors that are required for cap-dependent translation, conferring a selective advantage to the virus especially in times when the availability of such factors is low. Although the mechanism of translation initiation on the Hepatitis C virus (HCV) IRES is well established, modulation of the HCV IRES activity by both cellular and viral factors is not well understood. As the IRES is essential in the HCV life cycle and as such remains well conserved in an otherwise highly heterogenic virus, the process of HCV protein translation represents an attractive target in the development of novel antivirals. This review will focus on the mechanisms of HCV protein translation and how this process is postulated to be modulated by cis-acting viral factors, as well as trans-acting viral and cellular factors. Numerous therapeutic approaches investigated in targeting HCV protein translation for the development of novel antivirals will also be discussed.
Collapse
Affiliation(s)
- Brett Hoffman
- Vaccine and Infectious Disease Organization/International Vaccine Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | |
Collapse
|
18
|
Turnbough CL. Regulation of gene expression by reiterative transcription. Curr Opin Microbiol 2011; 14:142-7. [PMID: 21334966 DOI: 10.1016/j.mib.2011.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
Abstract
Gene regulation involves many different types of transcription control mechanisms, including mechanisms based on reiterative transcription in which nucleotides are repetitively added to the 3' end of a nascent transcript due to upstream transcript slippage. In these mechanisms, reiterative transcription is typically modulated by interactions between RNA polymerase and its nucleoside triphosphate substrates without the involvement of regulatory proteins. This review describes the current state of knowledge of gene regulation involving reiterative transcription. It focuses on the methods by which reiterative transcription is controlled and emphasizes the different fates of transcripts produced by this reaction. The review also includes a discussion of possible new and fundamentally different mechanisms of gene regulation that rely on conditional reiterative transcription.
Collapse
Affiliation(s)
- Charles L Turnbough
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA.
| |
Collapse
|
19
|
Qureshi H, Qazi R, Hamid S, Qureshi SA. Identification of immunogenic regions within the alternative reading frame protein of hepatitis C virus (genotype 3). Eur J Clin Microbiol Infect Dis 2011; 30:1075-83. [DOI: 10.1007/s10096-011-1194-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 01/25/2011] [Indexed: 01/29/2023]
|
20
|
Synonymous mutations in the core gene are linked to unusual serological profile in hepatitis C virus infection. PLoS One 2011; 6:e15871. [PMID: 21283512 PMCID: PMC3017048 DOI: 10.1371/journal.pone.0015871] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 11/25/2010] [Indexed: 01/18/2023] Open
Abstract
The biological role of the protein encoded by the alternative open reading frame (core+1/ARF) of the Hepatitis C virus (HCV) genome remains elusive, as does the significance of the production of corresponding antibodies in HCV infection. We investigated the prevalence of anti-core and anti-core+1/ARFP antibodies in HCV-positive blood donors from Cambodia, using peptide and recombinant protein-based ELISAs. We detected unusual serological profiles in 3 out of 58 HCV positive plasma of genotype 1a. These patients were negative for anti-core antibodies by commercial and peptide-based assays using C-terminal fragments of core but reacted by Western Blot with full-length core protein. All three patients had high levels of anti-core+1/ARFP antibodies. Cloning of the cDNA that corresponds to the core-coding region from these sera resulted in the expression of both core and core+1/ARFP in mammalian cells. The core protein exhibited high amino-acid homology with a consensus HCV1a sequence. However, 10 identical synonymous mutations were found, and 7 were located in the aa(99–124) region of core. All mutations concerned the third base of a codon, and 5/10 represented a T>C mutation. Prediction analyses of the RNA secondary structure revealed conformational changes within the stem-loop region that contains the core+1/ARFP internal AUG initiator at position 85/87. Using the luciferase tagging approach, we showed that core+1/ARFP expression is more efficient from such a sequence than from the prototype HCV1a RNA. We provide additional evidence of the existence of core+1/ARFP in vivo and new data concerning expression of HCV core protein. We show that HCV patients who do not produce normal anti-core antibodies have unusually high levels of antit-core+1/ARFP and harbour several identical synonymous mutations in the core and core+1/ARFP coding region that result in major changes in predicted RNA structure. Such HCV variants may favour core+1/ARFP production during HCV infection.
Collapse
|
21
|
Internal translation initiation stimulates expression of the ARF/core+1 open reading frame of HCV genotype 1b. Virus Res 2010; 155:213-20. [PMID: 20959129 DOI: 10.1016/j.virusres.2010.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/01/2010] [Accepted: 10/06/2010] [Indexed: 01/02/2023]
Abstract
The hepatitis C virus possesses an alternative open reading frame overlapping the Core gene, whose products are referred to as Core+1 or alternative reading frame (ARF) or F protein(s). Extensive studies on genotype HCV-1a demonstrated that ribosomal frameshifting supports the synthesis of core+1 protein, when ten consecutive As are present within core codons 9-11 whereas, in the absence of this motif, expression of the core+1 ORF is mediated mainly by internal translation initiation. However, in HCV-1b, no Core+1 isoforms produced by internal translation initiation have been described. Using constructs which contain the Core/Core+1(342-770) region from previously described HCV-1b clinical isolates from liver biopsies, we provide evidence for the synthesis of Core+1 proteins by internal translation initiation in transiently transfected mammalian cells using nuclear or cytoplasmic expression systems. Site directed mutagenesis analyses revealed that (a) the synthesis of Core+1 proteins is independent from the polyprotein expression, as we observed an increase of Core+1 protein expression from constructs lacking the polyprotein translation initiator, (b) the main Core+1 product is expressed from AUG(85), similarly to the Core+1/S protein of HCV-1a, (c) synthesis of Core+1 isoforms is also mediated from GUG(58) or under certain conditions GUG(26) internal codons, albeit at lower efficiency. Finally, comparable to HCV-1a Core+1 proteins, the HCV-1b Core+1 products are negatively regulated by core expression and the proteaosomal pathway. The expression of Core+1 ORF from HCV-1b clinical isolates and the preservation of translation initiation mechanism that stimulates its expression encourage investigating the role of these proteins in HCV pathogenesis.
Collapse
|
22
|
Transcript Slippage and Recoding. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2010. [DOI: 10.1007/978-0-387-89382-2_19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
23
|
Vassilaki N, Mavromara P. The HCV ARFP/F/core+1 protein: production and functional analysis of an unconventional viral product. IUBMB Life 2009; 61:739-52. [PMID: 19548320 DOI: 10.1002/iub.201] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hepatitis C virus (HCV) is an enveloped positive-strand RNA virus of the Flaviviridae family. It has a genome of about 9,600 nucleotides encoding a large polyprotein (about 3,000 amino acids) that is processed by cellular and viral proteases into at least 10 structural and nonstructural viral proteins. A novel HCV protein has also been identified by our laboratory and others. This protein--known as ARFP (alternative reading frame protein), F (for frameshift) or core+1 (to indicate the position) protein--is synthesized by an open reading frame overlapping the core gene at nucleotide +1 (core+1 ORF). However, almost 10 years after its discovery, we still know little of the biological role of the ARFP/F/core+1 protein. Abolishing core+1 protein production has no affect on HCV replication in cell culture or uPA-SCID mice, suggesting that core+1 protein is probably not important for the HCV reproductive cycle. However, the detection of specific anti-core+1 antibodies and T-cell responses in HCV-infected patients, as reported by many independent laboratories, provides strong evidence that this protein is produced in vivo. Furthermore, analyses of the HCV sequences isolated from patients with hepatocellular carcinoma and in vitro studies have provided strong preliminary evidence to suggest that core+1 protein plays a role in advanced liver disease and liver cancer. The available in vitro data also suggest that certain core function proteins may depend on production of the core+1 protein. We describe here the discovery of the various forms of the core+1 protein and what is currently known about the mechanisms of their production and their biochemical and functional properties. We also provide a detailed summary of the results of patient-based research.
Collapse
Affiliation(s)
- Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece.
| | | |
Collapse
|
24
|
Green fluorescent protein – Tagged HCV non-enveloped capsid like particles: Development of a new tool for tracking HCV core uptake. Biochimie 2009; 91:903-15. [DOI: 10.1016/j.biochi.2009.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 04/15/2009] [Indexed: 12/30/2022]
|
25
|
Internal initiation stimulates production of p8 minicore, a member of a newly discovered family of hepatitis C virus core protein isoforms. J Virol 2009; 83:3104-14. [PMID: 19129450 DOI: 10.1128/jvi.01679-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The hepatitis C virus (HCV) core gene is more conserved at the nucleic acid level than is necessary to preserve the sequence of the core protein, suggesting that it contains information for additional functions. We used a battery of anticore antibodies to test the hypothesis that the core gene directs the synthesis of core protein isoforms. Infectious viruses, replicons, and RNA transcripts expressed a p8 minicore containing the C-terminal portion of the p21 core protein and lacking the N-terminal portion. An interferon resistance mutation, U271A, which creates an AUG at codon 91, upregulated p8 expression in Con1 replicons, suggesting that p8 is produced by an internal initiation event and that 91-AUG is the preferred, but not the required, initiation codon. Synthesis of p8 was independent of p21, as shown by the abundant production of p8 from transcripts containing an UAG stop codon that blocked p21 production. Three infectious viruses, JFH-1 (2a core), J6/JFH (2a core), and H77/JFH (1a core), and a bicistronic construct, Bi-H77/JFH, all expressed both p8 and larger isoforms. The family of minicores ranges in size from 8 to 14 kDa. All lack the N-terminal portion of the p21 core. In conclusion, the core gene contains an internal signal that stimulates the initiation of protein synthesis at or near codon 91, leading to the production of p8. Infectious viruses of both genotype 1 and 2 HCV express a family of larger isoforms, in addition to p8. Minicores lack significant portions of the RNA binding domain of p21 core. Studies are under way to determine their functions.
Collapse
|
26
|
Ratinier M, Boulant S, Crussard S, McLauchlan J, Lavergne JP. Subcellular localizations of the hepatitis C virus alternate reading frame proteins. Virus Res 2008; 139:106-10. [PMID: 18996421 DOI: 10.1016/j.virusres.2008.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 09/16/2008] [Accepted: 09/19/2008] [Indexed: 12/28/2022]
Abstract
Alternate reading frame proteins (ARFPs) resulting either from frameshifting, from transcriptional slippage or from internal initiation in the +1 open reading frame (ORF) of hepatitis C virus (HCV) core protein coding sequence have been described in vitro. As an approach to study the roles of these proteins, we investigate the subcellular localization of ARFPs fused with the green fluorescent protein (GFP) either at their N- or C-terminus. Most GFP fusion products have a diffuse localization, as revealed by confocal microscopy. One GFP chimeric protein, arising from internal initiation at codon 26 in the +1 ORF (ARFP(26-161)), is specifically targeted to mitochondria. Mitochondrial localization was confirmed by immunoblot with an anti-ARFP antibody of a mitochondria-enriched cellular fraction. Mitochondrial targeting of ARFP(26-161) mostly involved the N-terminal portion of the protein as revealed by the cellular localization of truncated mutants. Interestingly, ARFP(26-161) from both genotypes 1a and 1b, but not the protein from the genotype 2a JFH1 infectious sequence, exhibit mitochondrial localization. These results are the first concerning the cellular localization and the role of this HCV ARFP; they may serve as a platform for further studies on its mitochondrial effects and their role in the virus life cycle and pathogenesis.
Collapse
Affiliation(s)
- Maxime Ratinier
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS-Université de Lyon, IFR 128 Biosciences, 7 passage du Vercors, 69367 Lyon cedex 07, France
| | | | | | | | | |
Collapse
|
27
|
Abstract
RNA viruses exhibit increased mutation frequencies relative to other organisms. Recent work has attempted to exploit this unique feature by increasing the viral mutation frequency beyond an extinction threshold, an antiviral strategy known as lethal mutagenesis. A number of novel nucleoside analogs have been designed around this premise. Herein, we review the quasispecies nature of RNA viruses and survey the antiviral, biological and biochemical characteristics of mutagenic nucleoside analogs, including clinically-used ribavirin. Biological implications of modulating viral replication fidelity are discussed in the context of translating lethal mutagenesis into a clinically-useful antiviral strategy.
Collapse
Affiliation(s)
- Jason D Graci
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ 07080, USA, Tel.: +1 908 912 9249; Fax: +1 908 222 0567;
| | - Craig E Cameron
- The Pennsylvania State University, Department of Biochemistry & Molecular Biology, 201 Althouse Laboratory, University Park, PA 16802, USA, Tel:. +1 814 863 8705; Fax: +1 814 863 7024;
| |
Collapse
|
28
|
Abstract
Hepatitis C virus (HCV) F protein is encoded by the +1 reading frame of the viral genome. It overlaps with the core protein coding sequence, and multiple mechanisms for its expression have been proposed. The full-length F protein that is synthesized by translational ribosomal frameshift at codons 9 to 11 of the core protein sequence is a labile protein. By using a combination of genetic, biochemical, and cell biological approaches, we demonstrate that this HCV F protein can bind to the proteasome subunit protein alpha3, which reduces the F-protein level in cells in a dose-dependent manner. Deletion-mapping analysis identified amino acids 40 to 60 of the F protein as the alpha3-binding domain. This alpha3-binding domain of the F protein together with its upstream sequence could significantly destabilize the green fluorescent protein, an otherwise stable protein. Further analyses using an F-protein mutant lacking lysine and a cell line that contained a temperature-sensitive E1 ubiquitin-activating enzyme indicated that the degradation of the F protein was ubiquitin independent. Based on these observations as well as the observation that the F protein could be degraded directly by the 20S proteasome in vitro, we propose that the full-length HCV F protein as well as the F protein initiating from codon 26 is degraded by an ubiquitin-independent pathway that is mediated by the proteasome subunit alpha3. The ability of the F protein to bind to alpha3 raises the possibility that the HCV F protein may regulate protein degradation in cells.
Collapse
|