1
|
Wu Z, Luo D, Zhang S, Zhang C, Zhang Y, Chen M, Li X. A systematic review of southern rice black-streaked dwarf virus in the age of omics. PEST MANAGEMENT SCIENCE 2023; 79:3397-3407. [PMID: 37291065 DOI: 10.1002/ps.7605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/22/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Southern rice black-streaked dwarf virus (SRBSDV) is one of the most damaging rice viruses. The virus decreases rice quality and yield, and poses a serious threat to food security. From this perspective, this review performed a survey of published studies in recent years to understand the current status of SRBSDV and white-backed planthopper (WBPH, Sogatella furcifera) transmission processes in rice. Recent studies have shown that the interactions between viral virulence proteins and rice susceptibility factors shape the transmission of SRBSDV. Moreover, the transmission of SRBSDV is influenced by the interactions between viral virulence proteins and S. furcifera susceptibility factors. This review focused on the molecular mechanisms of key genes or proteins associated with SRBSDV infection in rice via the S. furcifera vector, and the host defense response mechanisms against viral infection. A sustainable control strategy using RNAi was summarized to address this pest. Finally, we also present a model for screening anti-SRBSDV inhibitors using viral proteins as targets. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Zilin Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Dan Luo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Shanqi Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Chun Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Yong Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Moxian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiangyang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| |
Collapse
|
2
|
Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). ANNALS OF BOTANY 2021; 128:281-299. [PMID: 33729490 PMCID: PMC8389469 DOI: 10.1093/aob/mcab042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
Collapse
Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, PR China
| | - Thomas Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
3
|
Zhao S, Wu Y, Wu J. Arms race between rice and viruses: a review of viral and host factors. Curr Opin Virol 2021; 47:38-44. [PMID: 33530035 DOI: 10.1016/j.coviro.2021.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/28/2022]
Abstract
Much is known about the molecular interactions between positive-strand RNA viruses and dicotyledon plants. However, many important viral pathogens of the monocotyledon rice crop contain negative-strand or double-strand RNA genomes. Recent studies have shown that virus-derived small-interfering RNAs (siRNAs), host microRNAs and phytohormones regulate antiviral responses in rice plants and that rice-infecting RNA viruses encode a diverse repertoire of multifunctional proteins with counter-defensive activities. Moreover, the interactions between viral virulence proteins and host susceptibility factors also shape the virus-rice arms race. This review will focus on these recent advances and discuss strategies and challenges in the translation of discoveries made on molecular virus-rice interactions into practical virus control measures.
Collapse
Affiliation(s)
- Shanshan Zhao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuansheng Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
4
|
Vivek AT, Zahra S, Kumar S. From current knowledge to best practice: A primer on viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants. Methods 2019; 183:30-37. [PMID: 31669354 DOI: 10.1016/j.ymeth.2019.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023] Open
Abstract
Plants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to answer fundamental questions in plant virology. Here, we present some basic concepts of virus-derived, small interfering RNA (vsiRNA) biogenesis in plants, optimization strategies, caveats, and best practices for efficient discovery and diagnosis of known as well as novel plant viruses/viroids using deep sequencing of small RNA (sRNA) pools.
Collapse
Affiliation(s)
- A T Vivek
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shafaque Zahra
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
5
|
Yao S, Yang Z, Yang R, Huang Y, Guo G, Kong X, Lan Y, Zhou T, Wang H, Wang W, Cao X, Wu J, Li Y. Transcriptional Regulation of miR528 by OsSPL9 Orchestrates Antiviral Response in Rice. MOLECULAR PLANT 2019; 12:1114-1122. [PMID: 31059826 DOI: 10.1016/j.molp.2019.04.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/15/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Many microRNAs (miRNAs) are critical regulators of plant antiviral defense. However, little is known about how these miRNAs respond to virus invasion at the transcriptional level. We previously show that defense against Rice stripe virus (RSV) invasion entailed a reduction of miR528 accumulation in rice, alleviating miR528-mediated degradation of L-Ascorbate Oxidase (AO) mRNA and bolstering the antiviral activity of AO. Here we show that the miR528-AO defense module is regulated by the transcription factor SPL9. SPL9 displayed high-affinity binding to specific motifs within the promoter region of miR528 and activated the expression of miR528 gene in vivo. Loss-of-function mutations in SPL9 caused a significant reduction in miR528 accumulation but a substantial increase of AO mRNA, resulting in enhanced plant resistance to RSV. Conversely, transgenic overexpression of SPL9 stimulated the expression of miR528 gene, hence lowering the level of AO mRNA and compromising rice defense against RSV. Importantly, gain in RSV susceptibility did not occur when SPL9 was overexpressed in mir528 loss-of-function mutants, or in transgenic rice expressing a miR528-resistant AO. Taken together, the finding of SPL9-mediated transcriptional activation of miR528 expression adds a new regulatory layer to the miR528-AO antiviral defense pathway.
Collapse
Affiliation(s)
- Shengze Yao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Rongxin Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Huang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ge Guo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiangyue Kong
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - He Wang
- Rice Research Institute and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenming Wang
- Rice Research Institute and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
6
|
Sabbadini S, Ricci A, Limera C, Baldoni D, Capriotti L, Mezzetti B. Factors Affecting the Regeneration, via Organogenesis, and the Selection of Transgenic Calli in the Peach Rootstock Hansen 536 ( Prunus persica × Prunus amygdalus) to Express an RNAi Construct against PPV Virus. PLANTS (BASEL, SWITZERLAND) 2019; 8:E178. [PMID: 31213013 PMCID: PMC6631258 DOI: 10.3390/plants8060178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 01/27/2023]
Abstract
Prunus spp. is one of the most recalcitrant fruit tree species in terms of in vitro regeneration and transformation, mostly when mature tissues are used as explants. The present study describes the in vitro regeneration via indirect organogenesis, and Agrobacterium tumefaciens-mediated transformation of the peach rootstock Hansen 536 (Prunus persica × Prunus amygdalus) through the use of meristematic bulks (MBs) as starting explants. Efficient adventitious shoot regeneration was obtained when Hansen 536 MBs were cultured on an optimized medium consisting of modified McCown Woody Plant medium (WPM) enriched with 4.4 M 6-Benzyladenine (BA), 0.1 M 1-Naphthaleneacetic acid (NAA) and 6.0 g L-1 plant agar S1000 (B&V). MB slices were used later as starting explants for Agrobacterium-mediated transformation to introduce an RNAi construct "ihp35S-PPV194" against PPV virus. Transgenic events were identified by both green fluorescent protein (GFP) screening and kanamycin selection at different concentrations (0, 17 or 42 M). GFP-fluorescent proliferating callus lines were selected and confirmed to stably express the ihp35S-PPV194::eGFP gene construct by molecular analysis. Although shoot regeneration from these transgenic calli has not been obtained yet, this represents one of the few examples of successful attempts in peach genetic transformation from somatic tissues, and also serves as a useful in vitro system for future gene functional analysis in peach.
Collapse
Affiliation(s)
- Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Angela Ricci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Cecilia Limera
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Dania Baldoni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Luca Capriotti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| |
Collapse
|
7
|
RNA-Targeted Antiviral Immunity: More Than Just RNA Silencing. Trends Microbiol 2019; 27:792-805. [PMID: 31213342 DOI: 10.1016/j.tim.2019.05.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 11/21/2022]
Abstract
RNA silencing is a fundamental, evolutionarily conserved mechanism that regulates gene expression in eukaryotes. It also functions as a primary immune defense in microbes, such as viruses in plants. In addition to RNA silencing, RNA decay and RNA quality-control pathways are also two ancestral forms of intrinsic antiviral immunity, and the three RNA-targeted pathways may operate cooperatively for their antiviral function. Plant viruses encode viral suppressors of RNA silencing (VSRs) to suppress RNA silencing and facilitate virus infection. In response, plants may activate a counter-counter-defense mechanism to cope with VSR-mediated RNA silencing suppression. In this review, we summarize current knowledge of RNA silencing, RNA decay, and RNA quality control in antiviral defense, and highlight the mechanisms by which viruses compromise RNA-targeted immunity for their infection and survival in plants.
Collapse
|
8
|
Gebert D, Jehn J, Rosenkranz D. Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life. Open Biol 2019; 9:190020. [PMID: 31138098 PMCID: PMC6544989 DOI: 10.1098/rsob.190020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that, in some cases, selection favours more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and whether this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analysing a set of 1 million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low, RNA structuredness significantly more often than expected by chance. Taken together, we demonstrate that selection for high and low levels of secondary structure is a widespread phenomenon. Our results provide another line of evidence that synonymous mutations are less neutral than commonly thought, which is of importance for many evolutionary models.
Collapse
Affiliation(s)
- Daniel Gebert
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| | - Julia Jehn
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| |
Collapse
|
9
|
Yang Z, Li Y. Dissection of RNAi-based antiviral immunity in plants. Curr Opin Virol 2018; 32:88-99. [PMID: 30388659 DOI: 10.1016/j.coviro.2018.08.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 10/28/2022]
Abstract
RNA interference (RNAi)-based antiviral defense is a small RNA-dependent repression mechanism of plants to against viruses. Although the core components of antiviral RNAi are well known, it is unclear whether additional factors exist that regulate RNAi. Recently, a forward genetic screen identified two novel components of antiviral RNAi, providing important insights into the antiviral RNAi mechanism. Meanwhile, it was discovered that microRNAs make important contributions to host antiviral RNAi. On the other hand, to counteract host antiviral RNAi, most viruses encode viral suppressors of RNA silencing (VSRs). Recent studies have revealed the multiple functions of VSRs and the intricate interactions between plant hosts and viruses. These findings add to our knowledge of the sophisticated host antiviral defense mechanism in plants. Ongoing molecular functional studies will improve our understanding of the co-evolutionary arms race between viruses and plants, and thereby provide key information for the development of plant antiviral strategies.
Collapse
Affiliation(s)
- Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|