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Vermeulen A, Takken FLW, Sánchez-Camargo VA. Translation Arrest: A Key Player in Plant Antiviral Response. Genes (Basel) 2023; 14:1293. [PMID: 37372472 DOI: 10.3390/genes14061293] [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: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation of nucleotide-binding domain leucine-rich repeat (NLR) receptors. RNAi is associated with viral symptom recovery through translational repression and transcript degradation following recognition of viral double-stranded RNA produced during infection. NLR-mediated immunity is induced upon (in)direct recognition of a viral protein by an NLR receptor, triggering either a hypersensitive response (HR) or an extreme resistance response (ER). During ER, host cell death is not apparent, and it has been proposed that this resistance is mediated by a translational arrest (TA) of viral transcripts. Recent research indicates that translational repression plays a crucial role in plant antiviral resistance. This paper reviews current knowledge on viral translational repression during viral recovery and NLR-mediated immunity. Our findings are summarized in a model detailing the pathways and processes leading to translational arrest of plant viruses. This model can serve as a framework to formulate hypotheses on how TA halts viral replication, inspiring new leads for the development of antiviral resistance in crops.
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Affiliation(s)
- Annemarie Vermeulen
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Victor A Sánchez-Camargo
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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Arif M, Atta S, Bashir MA, Hussain A, Khan MI, Farooq S, Hannan A, Islam SU, Umar UUD, Khan M, Lin W, Hashem M, Alamri S, Wu Z. Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses. Methods 2020; 183:43-49. [PMID: 31759050 DOI: 10.1016/j.ymeth.2019.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/16/2019] [Indexed: 12/31/2022] Open
Abstract
Geminiviruses constitute a family of plant viruses with characteristic twinned quasi-icosahedral virions and a small circular DNA genome. Geminiviruses, especially begomoviruses, cause substantial economic losses in tropical and subtropical regions globally. Geminiviruses use the host's transcriptional mechanisms to synthesize their mRNAs. They are considered as an attractive model to understand the transcription mechanism of their host plants. Experiments were conducted to identify transcriptional start sites (TSSs) of the three begomoviruses, i.e., Cotton leaf curl Multan virus (CLCuMuV), Corchorus yellow vein virus (CoYVV), and Ramie mosaic virus (RamV). We first rub-inoculated Rice stripe tenuivirus (RSV), a segmented negative-sense RNA virus that uses cap-snatching to produce capped viral mRNAs, into N. benthamiana. After the inoculation, RSV-infected N. benthamiana were super-infected by CoYVV, CLCuMuV, or RamV, respectively. The capped-RNA leaders snatched by RSV were obtained by determining the 5'-ends of RSV mRNA with high throughput sequencing. Afterwards, snatched capped-RNA leaders of RSV were mapped onto the genome of each begomovirus and those matching the begomoviral genome were considered to come from the 5' ends of assumed begomoviral mRNAs. In this way, TSSs of begomoviruses were obtained. After mapping these TSSs onto the genome of the respective begomovirus, it was found very commonly that a begomovirus can use many different TSSs to transcribe the same gene, producing many different mRNA isoforms containing the corresponding open reading frames (ORFs).
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Affiliation(s)
- Muhammad Arif
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Sagheer Atta
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Muhammad Amjad Bashir
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Ansar Hussain
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Muhammad Ifnan Khan
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Shahid Farooq
- Department of Plant Protection, Faculty of Agriculture, Harran University, Sanliurfa 63200, Turkey
| | - Abdul Hannan
- Department of Botany, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Saif Ul Islam
- Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ummad Ud Din Umar
- Department of Plant Pathology, Bahauddin Zakariya University, Multan, Punjab 60800, Pakistan
| | - Mehran Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Wenzhong Lin
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mohamed Hashem
- King Khalid University, College of Science, Department of Biology, Abha 61413, Saudi Arabia; Assiut University, Faculty of Science, Botany and Microbiology Department, Assiut, Egypt
| | - Saad Alamri
- King Khalid University, College of Science, Department of Biology, Abha 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Lin W, Wu R, Qiu P, Jing Jin, Yang Y, Wang J, Lin Z, Zhang J, Wu Z, Du Z. A convenient in vivo cap donor delivery system to investigate the cap snatching of plant bunyaviruses. Virology 2020; 539:114-120. [PMID: 31710910 DOI: 10.1016/j.virol.2019.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/19/2023]
Abstract
Like their animal-infecting counterparts, plant bunyaviruses use capped RNA leaders cleaved from host cellular mRNAs to prime viral genome transcription in a process called cap-snatching, but in vivo systems to investigate the details of this process are lacking for them. Here, we report that Rice stripe tenuivirus (RSV) and Tomato spotted wilt tospovirus (TSWV) cleave capped RNA leaders from mRNAs transiently expressed by agroinfiltration, which makes it possible to artificially deliver defined cap donors to the two plant bunyaviruses with unprecedented convenience. With this system, some ideas regarding how plant bunyaviruses select and use capped RNA leaders can be tested easily. We were also able to obtain clear evidence that the capped RNA leaders selected by TSWV are generally longer than those by RSV. TSWV frequently uses the prime-and-realign mechanism in transcription primed by capped RNA leaders shorter than a certain length, like that has been demonstrated recently for RSV.
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Affiliation(s)
- Wenzhong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Ran Wu
- Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Ping Qiu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Jing Jin
- Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Yunyue Yang
- Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Jinglin Wang
- Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Zhonglong Lin
- China Tobacco Corporation Yunnan Company, Kunming, 650001, China
| | - Jie Zhang
- Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Zujian Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China.
| | - Zhenguo Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Plant virus research institute, Fujian Agricultural and Forestry University, Fuzhou, 350002, China.
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Lin W, Qiu P, Jin J, Liu S, Ul Islam S, Yang J, Zhang J, Kormelink R, Du Z, Wu Z. The Cap Snatching of Segmented Negative Sense RNA Viruses as a Tool to Map the Transcription Start Sites of Heterologous Co-infecting Viruses. Front Microbiol 2017; 8:2519. [PMID: 29312219 PMCID: PMC5735111 DOI: 10.3389/fmicb.2017.02519] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/04/2017] [Indexed: 01/06/2023] Open
Abstract
Identification of the transcription start sites (TSSs) of a virus is of great importance to understand and dissect the mechanism of viral genome transcription but this often requires costly and laborious experiments. Many segmented negative-sense RNA viruses (sNSVs) cleave capped leader sequences from a large variety of mRNAs and use these cleaved leaders as primers for transcription in a conserved process called cap snatching. The recent developments in high-throughput sequencing have made it possible to determine most, if not all, of the capped RNAs snatched by a sNSV. Here, we show that rice stripe tenuivirus (RSV), a plant-infecting sNSV, co-infects Nicotiana benthamiana with two different begomoviruses and snatches capped leader sequences from their mRNAs. By determining the 5' termini of a single RSV mRNA with high-throughput sequencing, the 5' ends of almost all the mRNAs of the co-infecting begomoviruses could be identified and mapped on their genomes. The findings in this study provide support for the using of the cap snatching of sNSVs as a tool to map viral TSSs.
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Affiliation(s)
- Wenzhong Lin
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Qiu
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Jin
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shunmin Liu
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Saif Ul Islam
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinguang Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jie Zhang
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
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Liu X, Xiong G, Qiu P, Du Z, Kormelink R, Zheng L, Zhang J, Ding X, Yang L, Zhang S, Wu Z. Inherent properties not conserved in other tenuiviruses increase priming and realignment cycles during transcription of Rice stripe virus. Virology 2016; 496:287-298. [PMID: 27393974 DOI: 10.1016/j.virol.2016.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/29/2022]
Abstract
Two tenuiviruses Rice stripe virus (RSV) and Rice grassy stunt virus (RGSV) were found to co-infect rice with the same reovirus Rice ragged stunt virus (RRSV). During the co-infection, both tenuiviruses recruited 10-21 nucleotides sized capped-RNA leaders from the RRSV. A total of 245 and 102 RRSV-RGSV and RRSV-RSV chimeric mRNA clones, respectively, were sequenced. An analysis of the sequences suggested a scenario consistent with previously reported data on related viruses, in which capped leader RNAs having a 3' end complementary to the viral template are preferred and upon base pairing the leaders prime processive transcription directly or after one to several cycles of priming and realignment (repetitive prime-and-realign). Interestingly, RSV appeared to have a higher tendency to use repetitive prime-and-realign than RGSV even with the same leader derived from the same RRSV RNA. Combining with relevant data reported previously, this points towards an intrinsic feature of RSV.
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Affiliation(s)
- Xiaojuan Liu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Guihong Xiong
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ping Qiu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Luping Zheng
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jie Zhang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xinlun Ding
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Liang Yang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Songbai Zhang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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6
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Koppstein D, Ashour J, Bartel DP. Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation. Nucleic Acids Res 2015; 43:5052-64. [PMID: 25901029 PMCID: PMC4446424 DOI: 10.1093/nar/gkv333] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/01/2015] [Indexed: 12/15/2022] Open
Abstract
The influenza polymerase cleaves host RNAs ∼10–13 nucleotides downstream of their 5′ ends and uses this capped fragment to prime viral mRNA synthesis. To better understand this process of cap snatching, we used high-throughput sequencing to determine the 5′ ends of A/WSN/33 (H1N1) influenza mRNAs. The sequences provided clear evidence for nascent-chain realignment during transcription initiation and revealed a strong influence of the viral template on the frequency of realignment. After accounting for the extra nucleotides inserted through realignment, analysis of the capped fragments indicated that the different viral mRNAs were each prepended with a common set of sequences and that the polymerase often cleaved host RNAs after a purine and often primed transcription on a single base pair to either the terminal or penultimate residue of the viral template. We also developed a bioinformatic approach to identify the targeted host transcripts despite limited information content within snatched fragments and found that small nuclear RNAs and small nucleolar RNAs contributed the most abundant capped leaders. These results provide insight into the mechanism of viral transcription initiation and reveal the diversity of the cap-snatched repertoire, showing that noncoding transcripts as well as mRNAs are used to make influenza mRNAs.
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Affiliation(s)
- David Koppstein
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Whitehead Institute of Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA
| | - Joseph Ashour
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Whitehead Institute of Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - David P Bartel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Whitehead Institute of Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA
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7
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Olal D, Dick A, Woods VL, Liu T, Li S, Devignot S, Weber F, Saphire EO, Daumke O. Structural insights into RNA encapsidation and helical assembly of the Toscana virus nucleoprotein. Nucleic Acids Res 2014; 42:6025-37. [PMID: 24688060 PMCID: PMC4027202 DOI: 10.1093/nar/gku229] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Toscana virus is an emerging bunyavirus in Mediterranean Europe where it accounts for 80% of pediatric meningitis cases during the summer. The negative-strand ribonucleic acid (RNA) genome of the virus is wrapped around the virally encoded nucleoprotein N to form the ribonucleoprotein complex (RNP). We determined crystal structures of hexameric N alone (apo) and in complex with a nonameric single-stranded RNA. RNA is sequestered in a sequence-independent fashion in a deep groove inside the hexamer. At the junction between two adjacent copies of Ns, RNA binding induced an inter-subunit rotation, which opened the RNA-binding tunnel and created a new assembly interface at the outside of the hexamer. Based on these findings, we suggest a structural model for how binding of RNA to N promotes the formation of helical RNPs, which are a characteristic hallmark of many negative-strand RNA viruses.
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Affiliation(s)
- Daniel Olal
- Max Delbrück Center for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125 Berlin, Germany Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexej Dick
- Max Delbrück Center for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Virgil L Woods
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tong Liu
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sheng Li
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Stephanie Devignot
- Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Friedemann Weber
- Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Daumke
- Max Delbrück Center for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125 Berlin, Germany Freie Universität Berlin, Biochemistry, Takustrasse 6, 14195 Berlin, Germany
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Walia JJ, Falk BW. Fig mosaic virus mRNAs show generation by cap-snatching. Virology 2012; 426:162-6. [PMID: 22356803 DOI: 10.1016/j.virol.2012.01.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/09/2011] [Accepted: 01/28/2012] [Indexed: 10/28/2022]
Abstract
Fig mosaic virus (FMV), a member of the newly described genus Emaravirus, has four negative-sense single-stranded genomic RNAs, and each codes for a single protein in the viral complementary RNA (vcRNA). In this study we show that FMV mRNAs for genome segments 2 and 3 contain short (12-18 nucleotides) heterogeneous nucleotide leader sequences at their 5' termini. Furthermore, by using the high affinity cap binding protein eIF4E(K119A), we also determined that a 5' cap is present on a population of the FMV positive-sense RNAs, presumably as a result of cap-snatching. Northern hybridization results showed that the 5' capped RNA3 segments are slightly smaller than the homologous vcRNA3 and are not polyadenylated. These data suggest that FMV generates 5' capped mRNAs via cap-snatching, similar to strategies used by other negative-sense multipartite ssRNA viruses.
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Affiliation(s)
- Jeewan Jyot Walia
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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9
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Yao M, Zhang T, Zhou T, Zhou Y, Zhou X, Tao X. Repetitive prime-and-realign mechanism converts short capped RNA leaders into longer ones that may be more suitable for elongation during rice stripe virus transcription initiation. J Gen Virol 2012; 93:194-202. [PMID: 21918010 DOI: 10.1099/vir.0.033902-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cucumber mosaic virus (CMV) RNAs were found to serve as cap donors for rice stripe virus (RSV) transcription initiation during their co-infection of Nicotiana benthamiana. The 5' end of CMV RNAs was cleaved preferentially at residues that had multiple-base complementarity to the 3' end of the RSV template. The length requirement for CMV capped primers to be suitable for elongation varied between 12 and 20 nt, and those of 12-16 nt were optimal for elongation and generated more CMV-RSV chimeric mRNA transcripts. The original cap donors that were cleaved from CMV RNAs were predominantly short (10-13 nt). However, the CMV capped RNA leaders that underwent long-distance elongation were found to contain up to five repetitions of additional AC dinucleotides. Sequence analysis revealed that these AC dinucleotides were used to increase the size of short cap donors in multiple prime-and-realign cycles. Each prime-and-realign cycle added an AC dinucleotide onto the capped RNA leaders; thus, the original cap donors were gradually converted to longer capped RNA leaders (of 12-20 nt). Interestingly, the original 10 nt (or 11 nt) cap donor cleaved from CMV RNA1/2 did not undergo direct extension; only capped RNA leaders that had been increased to ≥12 nt were used for direct elongation. These findings suggest that this repetitive priming and realignment may serve to convert short capped CMV RNA leaders into longer, more suitable sizes to render a more stabilized transcription complex for elongation during RSV transcription initiation.
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Affiliation(s)
- Min Yao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tianqi Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, PR China
| | - Xiaorong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
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10
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Brown BA, Panganiban AT. Identification of a region of hantavirus nucleocapsid protein required for RNA chaperone activity. RNA Biol 2010; 7:830-7. [PMID: 21378500 DOI: 10.4161/rna.7.6.13862] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Sin Nombre hantavirus (SNV) is a New World hantavirus and causes hantavirus cardiopulmonary syndrome. The viral nucleocapsid protein (N) is an RNA chaperone and has multiple functions important in virus replication. The three negative sense RNA segments of hantaviruses form panhandle structures through imperfect hydrogen bonding of the 5' and 3' termini, and the chaperone activity of N can mediate correct panhandle formation. N also functions during transcription and translation initiation and the chaperone activity of N is likely to be involved in aspects of these processes. Using a series of mutations in the N gene we identified a region of N required for chaperone activity. The N-terminal 100 amino acids of N contain a domain that is both necessary and sufficient for RNA chaperone activity. We propose that this region of N may reside in one of two potential states. First, the region may be highly disordered and function in N-mediated RNA chaperone activity. Alternatively, in trimeric form, the region likely becomes ordered and serves in high affinity vRNA panhandle recognition.
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Affiliation(s)
- Bradley A Brown
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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11
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Storage of cellular 5' mRNA caps in P bodies for viral cap-snatching. Proc Natl Acad Sci U S A 2008; 105:19294-9. [PMID: 19047634 DOI: 10.1073/pnas.0807211105] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The minus strand and ambisense segmented RNA viruses include multiple important human pathogens and are divided into three families, the Orthomyxoviridae, the Bunyaviridae, and the Arenaviridae. These viruses all initiate viral transcription through the process of "cap-snatching," which involves the acquisition of capped 5' oligonucleotides from cellular mRNA. Hantaviruses are emerging pathogenic viruses of the Bunyaviridae family that replicate in the cytoplasm of infected cells. Cellular mRNAs can be actively translated in polysomes or physically sequestered in cytoplasmic processing bodies (P bodies) where they are degraded or stored for subsequent translation. Here we show that the hantavirus nucleocapsid protein binds with high affinity to the 5' cap of cellular mRNAs, protecting the 5' cap from degradation. We also show that the hantavirus nucleocapsid protein accumulates in P bodies, where it sequesters protected 5' caps. P bodies then serve as a pool of primers during the initiation of viral mRNA synthesis by the viral polymerase. We propose that minus strand segmented viruses replicating in the cytoplasm have co-opted the normal degradation machinery of P bodies for storage of cellular caps. Our data also indicate that modification of the cap-snatching model is warranted to include a role for the nucleocapsid protein in cap acquisition and storage.
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12
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van Knippenberg I, Lamine M, Goldbach R, Kormelink R. Tomato spotted wilt virus transcriptase in vitro displays a preference for cap donors with multiple base complementarity to the viral template. Virology 2005; 335:122-30. [PMID: 15823611 DOI: 10.1016/j.virol.2005.01.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 01/05/2005] [Accepted: 01/31/2005] [Indexed: 11/20/2022]
Abstract
Transcription of segmented negative-strand RNA viruses is initiated by cap snatching: a host mRNA is cleaved generally at 10-20 nt from its 5' capped end and the resulting capped leader used to prime viral transcription. For Tomato spotted wilt virus (TSWV), type species of the plant-infecting Tospovirus genus within the Bunyaviridae, cap donors were previously shown to require a single base complementarity to the ultimate or penultimate viral template sequence. More recently, the occurrence in vitro of "re-snatching" of viral mRNAs, i.e., the use of viral mRNAs as cap donors, has been demonstrated for TSWV. To estimate the relative occurrence of re-snatching compared to snatching of host mRNAs, the use of cap donors with either single, double, or multiple complementarity to the viral template was analyzed in pair-wise competition in TSWV in vitro transcription assays. A strong preference was observed for multiple-basepairing donors.
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Affiliation(s)
- Ingeborg van Knippenberg
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709PD Wageningen, The Netherlands
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Abstract
Among the negative RNA viruses, ambisense RNA viruses or 'ambisense viruses' occupy a distinct niche. Ambisense viruses contain at least one ambisense RNA segment, i.e. an RNA that is in part of positive and in part of negative polarity. Because of this unique gene organization, one might expect ambisense RNA viruses to borrow expression strategies from both positive and negative RNA viruses. However, they have little in common with positive RNA viruses, but possess many features of negative RNA viruses. Transcription and/or replication of their RNAs appear generally to be coupled to translation. Such coupling might be important to ensure temporal control of gene expression, allowing the two genes of an ambisense RNA segment to be differently regulated. Ambisense viruses can infect one host asymptomatically and in certain cases, they can lethally infect two hosts of a different kingdom. A possible model to explain the differential behavior of a given virus in different hosts could be that perturbation of the translation machinery would lead to differences in the severity of symptoms.
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Affiliation(s)
- Marie Nguyen
- Institut Jacques Monod, 2 Place Jussieu-Tour 43, 75251 Paris, Cedex 05, France.
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Rao P, Yuan W, Krug RM. Crucial role of CA cleavage sites in the cap-snatching mechanism for initiating viral mRNA synthesis. EMBO J 2003; 22:1188-98. [PMID: 12606583 PMCID: PMC150342 DOI: 10.1093/emboj/cdg109] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In viral cap-snatching, the endonuclease intrinsic to the viral polymerase cleaves cellular capped RNAs to generate capped fragments that are primers for viral mRNA synthesis. Here we demonstrate that the influenza viral polymerase, which is assembled in human cells using recombinant proteins, effectively uses only CA-terminated capped fragments as primers for viral mRNA synthesis in vitro. Thus we provide the first in vitro system that mirrors the cap-snatching process occurring in vivo during virus infection. Further, we demonstrate that when a capped RNA substrate contains a CA cleavage site, the functions of virion RNA (vRNA) differ from those previously described: the 5' terminal sequence of vRNA alone is sufficient for endonuclease activation, and the 3' terminal sequence of vRNA functions solely as a template for mRNA synthesis. Consequently, we are able to identify the vRNA sequences that are required for each of these two separable functions. We present a new model for the influenza virus cap-snatching mechanism, which we postulate is a paradigm for the cap-snatching mechanisms of other segmented, negative-strand and ambisense RNA viruses.
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Affiliation(s)
| | | | - Robert M. Krug
- Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
Corresponding author e-mail:
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Duijsings D, Kormelink R, Goldbach R. In vivo analysis of the TSWV cap-snatching mechanism: single base complementarity and primer length requirements. EMBO J 2001; 20:2545-52. [PMID: 11350944 PMCID: PMC125463 DOI: 10.1093/emboj/20.10.2545] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2001] [Revised: 03/06/2001] [Accepted: 03/23/2001] [Indexed: 11/14/2022] Open
Abstract
Requirements for capped leader sequences for use during transcription initiation by tomato spotted wilt virus (TSWV) were tested using mutant alfalfa mosaic virus (AMV) RNAs as specific cap donors in transgenic Nicotiana tabacum plants expressing the AMV replicase proteins. Using a series of AMV RNA3 mutants modified in either the 5'-non-translated region or in the subgenomic RNA4 leader, sequence analysis revealed that cleaved leader lengths could vary between 13 and 18 nucleotides. Cleavage occurred preferentially at an A residue, suggesting a requirement for a single base complementarity with the TSWV RNA template, which could be confirmed by analyses of host mRNAs used in vivo as cap donors.
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Affiliation(s)
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD, Wageningen, The Netherlands
Corresponding author e-mail:
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Hammond J, Lecoq H, Raccah B. Epidemiological risks from mixed virus infections and transgenic plants expressing viral genes. Adv Virus Res 1999; 54:189-314. [PMID: 10547677 DOI: 10.1016/s0065-3527(08)60368-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- J Hammond
- USDA-ARS, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, Maryland 20705, USA
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Duijsings D, Kormelink R, Goldbach R. Alfalfa mosaic virus RNAs serve as cap donors for tomato spotted wilt virus transcription during coinfection of Nicotiana benthamiana. J Virol 1999; 73:5172-5. [PMID: 10233983 PMCID: PMC112565 DOI: 10.1128/jvi.73.6.5172-5175.1999] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tomato spotted wilt virus (TSWV) was shown to use alfalfa mosaic virus (AMV) RNAs as cap donors in vivo during a mixed infection in Nicotiana benthamiana. By use of nested reverse transcription-PCR, TSWV N and NSs mRNAs provided with capped leader sequences derived from all four AMV RNAs could be cloned and sequenced. The sequence specificity of the putative TSWV endonuclease involved is discussed.
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Affiliation(s)
- D Duijsings
- Laboratory of Virology, Wageningen Agricultural University, 6709 PD Wageningen, The Netherlands
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