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Wrzesińska-Krupa B, Obrępalska-Stęplowska A. Small non-coding satellite RNAs - the 'game changers' at the virus-host plant interaction? Biol Rev Camb Philos Soc 2024. [PMID: 39054260 DOI: 10.1111/brv.13125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/03/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Satellite RNAs (satRNAs) are RNA molecules associated with many plant viruses and fully dependent on them for replication, encapsidation, and movement within the plant or transmission from plant to plant. Their classification is based on their length, functional protein-coding capacity, and RNA structure (whether linear or circular). They have been of interest for a long time as some of them, in particular systems, cause significant changes in the pathogenesis and epidemiology of plant viruses. The outcomes of how satRNAs affect pathogenesis depend on the components of the pathosystem: host plant species or variety, virus species or even strain, and the sequence of satRNA. These can be additionally affected by biotic and abiotic factors, for example, environmental conditions such as the presence of their vectors or ambient temperature. satRNAs may interfere with primary metabolism, signalling, plant defence [including post-transcriptional gene silencing (PTGS)], as well as the efficiency of virus transmission from plant to plant. In recent years, due to wider access to high-throughput technologies and the extension of studies on satRNAs to include the involvement of external factors in plant-virus-satRNA systems, we are gaining a broader view of the consequences of the presence of these small molecules in viral infections. This review presents the state of the art of satRNA interactions with the helper virus and host plant as well as the influence of satRNAs on the insect vector's behaviour. Moreover, areas requiring further research are identified and knowledge gaps indicated.
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Affiliation(s)
- Barbara Wrzesińska-Krupa
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20, Poznań, 60-318, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20, Poznań, 60-318, Poland
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2
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Roossinck MJ. The Ups and Downs of an Out-of-the-Box Scientist with a Curious Mind. Annu Rev Virol 2022; 9:19-38. [PMID: 35512631 DOI: 10.1146/annurev-virology-100520-013446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
My early life was challenging, and not conducive to the study of science, but my first introduction to viruses was an epiphany for me. I spent the whole of my career dedicated to understanding viruses, driven largely by curiosity. This led me down many different avenues of study, and to work with many wonderful colleagues, most of whom remain friends. Some highlights of my career include the discovery of a mutualistic three-way symbiosis involving a virus, a fungus, and a plant; genetic mapping of a pathogenicity gene in tomato; uncovering a virus in 1,000-year-old corncobs; exploring virus biodiversity in wild plants; and establishing a system to use a fungal virus to understand the epidemiology of its host. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, USA;
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Badar U, Venkataraman S, AbouHaidar M, Hefferon K. Molecular interactions of plant viral satellites. Virus Genes 2020; 57:1-22. [PMID: 33226576 DOI: 10.1007/s11262-020-01806-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/24/2020] [Indexed: 12/18/2022]
Abstract
Plant viral satellites fall under the category of subviral agents. Their genomes are composed of small RNA or DNA molecules a few hundred nucleotides in length and contain an assortment of highly complex and overlapping functions. Each lacks the ability to either replicate or undergo encapsidation or both in the absence of a helper virus (HV). As the number of known satellites increases steadily, our knowledge regarding their sequence conservation strategies, means of replication and specific interactions with host and helper viruses is improving. This review demonstrates that the molecular interactions of these satellites are unique and highly complex, largely influenced by the highly specific host plants and helper viruses that they associate with. Circularized forms of single-stranded RNA are of particular interest, as they have recently been found to play a variety of novel cellular functions. Linear forms of satRNA are also of great significance as they may complement the helper virus genome in exacerbating symptoms, or in certain instances, actively compete against it, thus reducing symptom severity. This review serves to describe the current literature with respect to these molecular mechanisms in detail as well as to discuss recent insights into this emerging field in terms of evolution, classification and symptom development. The review concludes with a discussion of future steps in plant viral satellite research and development.
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Affiliation(s)
- Uzma Badar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Mounir AbouHaidar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Kathleen Hefferon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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4
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Shrestha N, Bujarski JJ. Long Noncoding RNAs in Plant Viroids and Viruses: A Review. Pathogens 2020; 9:E765. [PMID: 32961969 PMCID: PMC7559573 DOI: 10.3390/pathogens9090765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs.
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Affiliation(s)
- Nipin Shrestha
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA
| | - Józef J. Bujarski
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA
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5
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Bayne CF, Widawski ME, Gao F, Masab MH, Chattopadhyay M, Murawski AM, Sansevere RM, Lerner BD, Castillo RJ, Griesman T, Fu J, Hibben JK, Garcia-Perez AD, Simon AE, Kushner DB. SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants. Virology 2018; 520:137-152. [PMID: 29864677 DOI: 10.1016/j.virol.2018.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/06/2018] [Accepted: 05/12/2018] [Indexed: 11/19/2022]
Abstract
Noncoding RNAs use their sequence and/or structure to mediate function(s). The 5' portion (166 nt) of the 356-nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) was previously modeled to contain a central region with two stem-loops (H6 and H7) and a large connecting hairpin (H2). We now report that in vivo functional selection (SELEX) experiments assessing sequence/structure requirements in H2, H6, and H7 reveal that H6 loop sequence motifs were recovered at nonrandom rates and only some residues are proposed to base-pair with accessible complementary sequences within the 5' central region. In vitro SHAPE of SELEX winners indicates that the central region is heavily base-paired, such that along with the lower stem and H2 region, one extensive hairpin exists composing the entire 5' region. As these SELEX winners are highly fit, these characteristics facilitate satRNA amplification in association with TCV in plants.
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Affiliation(s)
- Charlie F Bayne
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Max E Widawski
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Mohammed H Masab
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Maitreyi Chattopadhyay
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | | | | | - Bryan D Lerner
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | | | - Trevor Griesman
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Jiantao Fu
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | | | | | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - David B Kushner
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
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Palukaitis P. Satellite RNAs and Satellite Viruses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:181-186. [PMID: 26551994 DOI: 10.1094/mpmi-10-15-0232-fi] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Satellite RNAs and satellite viruses are extraviral components that can affect either the pathogenicity, the accumulation, or both of their associated viruses while themselves being dependent on the associated viruses as helper viruses for their infection. Most of these satellite RNAs are noncoding RNAs, and in many cases, have been shown to alter the interaction of their helper viruses with their hosts. In only a few cases have the functions of these satellite RNAs in such interactions been studied in detail. In particular, work on the satellite RNAs of Cucumber mosaic virus and Turnip crinkle virus have provided novel insights into RNAs functioning as noncoding RNAs. These effects are described and potential roles for satellite RNAs in the processes involved in symptom intensification or attenuation are discussed. In most cases, models describing these roles involve some aspect of RNA silencing or its suppression, either directly or indirectly involving the particular satellite RNA.
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Affiliation(s)
- Peter Palukaitis
- Department of Horticultural Sciences, Seoul Women's University, 621 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
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Shimura H, Masuta C. Plant subviral RNAs as a long noncoding RNA (lncRNA): Analogy with animal lncRNAs in host-virus interactions. Virus Res 2015; 212:25-9. [PMID: 26116900 DOI: 10.1016/j.virusres.2015.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 12/16/2022]
Abstract
Satellite RNAs (satRNAs) and viroids belong to the group called subviral agents and are the smallest pathogens of plants. In general, small satRNAs and viroids are 300-400 nt in size and do not encode any functional proteins; they are thus regarded as so-called long noncoding RNAs (lncRNAs). These lncRNAs are receiving great attention as a new RNA class involved in gene regulation to control important biological processes such as gene transcription and epigenetic regulation. A substantial number of lncRNAs in animal cells have been found to play important roles in the interactions between a virus and its host. We here discuss the pathogenicity of subviral RNAs (especially satRNAs) in plant cells and their functions as lncRNAs associated with viral diseases, using animal lncRNAs as an analogy. Because, unlike animal lncRNAs, plant subviral RNAs can replicate and accumulate at very high levels in infected cells, we here considered the unique possibility that the RNA silencing machinery of plants, an important defense mechanism against virus infection, may have brought about the replication ability of subviral molecules. In addition, we also discuss the possibility that satRNAs may have arisen from plant-virus interactions in virus-infected cells. Understanding the molecular functions of these unique lncRNAs in plants will enable us to reveal the most plausible origins of these subviral RNAs.
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Affiliation(s)
- Hanako Shimura
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo 060-8589, Japan.
| | - Chikara Masuta
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo 060-8589, Japan.
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Xu P, Wang H, Coker F, Ma JY, Tang Y, Taylor M, Roossinck MJ. Genetic loci controlling lethal cell death in tomato caused by viral satellite RNA infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1034-1044. [PMID: 22746824 DOI: 10.1094/mpmi-01-12-0004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cucumber mosaic virus (CMV) associated with D satellite RNA (satRNA) causes lethal systemic necrosis (LSN) in tomato (Solanum lycopersicum), which involves programmed cell death. No resistance to this disease has been found in tomato. We obtained a line of wild tomato, S. habrochaitis, with a homogeneous non-lethal response (NLR) to the infection. This line of S. habrochaitis was crossed with tomato to generate F1 plants that survived the infection with NLR, indicating that NLR is a dominant trait. The NLR trait was successfully passed on to the next generation. The phenotype and genotype segregation was analyzed in the first backcross population. The analyses indicate that the NLR trait is determined by quantitative trait loci (QTL). Major QTL associated with the NLR trait were mapped to chromosomes 5 and 12. Results from Northern blot and in situ hybridization analyses revealed that the F1 and S. habrochaitis plants accumulated minus-strand satRNA more slowly than tomato, and fewer vascular cells were infected. In addition, D satRNA-induced LSN in tomato is correlated with higher accumulation of the minus-strand satRNA compared with the accumulation of the minus strand of a non-necrogenic mutant D satRNA.
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Affiliation(s)
- Ping Xu
- The Samuel Robert Noble Foundation, Ardmore, OK, USA
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Abstract
Cucumber mosaic virus (CMV) is an important virus because of its agricultural impact in the Mediterranean Basin and worldwide, and also as a model for understanding plant-virus interactions. This review focuses on those areas where most progress has been made over the past decade in our understanding of CMV. Clearly, a deep understanding of the role of the recently described CMV 2b gene in suppression of host RNA silencing and viral virulence is the most important discovery. These findings have had an impact well beyond the virus itself, as the 2b gene is an important tool in the studies of eukaryotic gene regulation. Protein 2b was shown to be involved in most of the steps of the virus cycle and to interfere with several basal host defenses. Progress has also been made concerning the mechanisms of virus replication and movement. However, only a few host proteins that interact with viral proteins have been identified, making this an area of research where major efforts are still needed. Another area where major advances have been made is CMV population genetics, where contrasting results were obtained. On the one hand, CMV was shown to be prone to recombination and to show high genetic diversity based on sequence data of different isolates. On the other hand, populations did not exhibit high genetic variability either within plants, or even in a field and the nearby wild plants. The situation was partially clarified with the finding that severe bottlenecks occur during both virus movement within a plant and transmission between plants. Finally, novel studies were undertaken to elucidate mechanisms leading to selection in virus population, according to the host or its environment, opening a new research area in plant-virus coevolution.
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Betancourt M, Fraile A, García-Arenal F. Cucumber mosaic virus satellite RNAs that induce similar symptoms in melon plants show large differences in fitness. J Gen Virol 2011; 92:1930-1938. [PMID: 21562122 DOI: 10.1099/vir.0.032359-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two groups of Cucumber mosaic virus (CMV) satellite RNAs (satRNAs), necrogenic and non-necrogenic, can be differentiated according to the symptoms they cause in tomato plants, a host in which they also differ in fitness. In most other CMV hosts these CMV-satRNA cause similar symptoms. Here, we analyse whether they differ in traits determining their relative fitness in melon plants, in which the two groups of CMV-satRNAs cause similar symptoms. For this, ten necrogenic and ten non-necrogenic field satRNA genotypes were assayed with Fny-CMV as a helper virus. Neither type of CMV-satRNA modified Fny-CMV symptoms, and both types increased Fny-CMV virulence similarly, as measured by decreases in plant biomass and lifespan. Necrogenic and non-necrogenic satRNAs differed in their ability to multiply in melon tissues; necrogenic satRNAs accumulated to higher levels both in single infection and in competition with non-necrogenic satRNAs. Indeed, multiplication of some non-necrogenic satRNAs was undetectable. Transmission between hosts by aphids was less efficient for necrogenic satRNAs as a consequence of a more severe reduction of CMV accumulation in leaves. The effect of CMV accumulation on aphid transmission was not compensated for by differences in satRNA encapsidation efficiency or transmissibility to CMV progeny. Thus, necrogenic and non-necrogenic satRNAs differ in their relative fitness in melon, and trade-offs are apparent between the within-host and between-host components of satRNA fitness. Hence, CMV-satRNAs could have different evolutionary dynamics in CMV host-plant species in which they do not differ in pathogenicity.
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Affiliation(s)
- Mónica Betancourt
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
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Satellite RNAs and Satellite Viruses of Plants. Viruses 2009; 1:1325-50. [PMID: 21994595 PMCID: PMC3185516 DOI: 10.3390/v1031325] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 12/07/2009] [Accepted: 12/07/2009] [Indexed: 12/24/2022] Open
Abstract
The view that satellite RNAs (satRNAs) and satellite viruses are purely molecular parasites of their cognate helper viruses has changed. The molecular mechanisms underlying the synergistic and/or antagonistic interactions among satRNAs/satellite viruses, helper viruses, and host plants are beginning to be comprehended. This review aims to summarize the recent achievements in basic and practical research, with special emphasis on the involvement of RNA silencing mechanisms in the pathogenicity, population dynamics, and, possibly, the origin(s) of these subviral agents. With further research following current trends, the comprehensive understanding of satRNAs and satellite viruses could lead to new insights into the trilateral interactions among host plants, viruses, and satellites.
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12
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Afroz A, Khan MR, Ahsan N, Komatsu S. Comparative proteomic analysis of bacterial wilt susceptible and resistant tomato cultivars. Peptides 2009; 30:1600-7. [PMID: 19524626 DOI: 10.1016/j.peptides.2009.06.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Revised: 06/02/2009] [Accepted: 06/03/2009] [Indexed: 12/01/2022]
Abstract
To investigate the molecular mechanisms of bacterial resistance in susceptible and resistant cultivars of tomato, a proteomic approach was adopted. Four cultivars of tomato were selected on the basis of their response to bacterial (Pseudomonas solanacearum) inoculation wherein cultivar Roma and Riogarande, and cultivar Pusa Ruby and Pant Bahr were considered as resistant and susceptible cultivars, respectively. Proteins were extracted from leaves of 3-week-old seedlings of the four cultivars and separated by 2-DE. A total of nine proteins were found to be differentially expressed between the susceptible and resistant cultivars. Amino acid sequences of these proteins were determined with a protein sequencer. The identified proteins belongs to the categories of energy, protein destination and storage, and defense. Of these proteins, a 60kDa chaperonin and an apical membrane antigen were significantly upregulated in resistant cultivars compared with susceptible cultivars. Application of jasmonic acid and salicylic acid resulted in significant changes in levels of apical membrane antigen and protein disulfide-isomerase. Taken together, these results suggest that apical membrane antigen might be involved in bacterial resistance process through salicylic acid induced defense mechanism signaling in tomato plants.
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Affiliation(s)
- Amber Afroz
- National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Japan
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Xu P, Chen F, Mannas JP, Feldman T, Sumner LW, Roossinck MJ. Virus infection improves drought tolerance. THE NEW PHYTOLOGIST 2008; 180:911-21. [PMID: 18823313 DOI: 10.1111/j.1469-8137.2008.02627.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Viruses are obligate intracellular symbionts. Plant viruses are often discovered and studied as pathogenic parasites that cause diseases in agricultural plants. However, here it is shown that viruses can extend survival of their hosts under conditions of abiotic stress that could benefit hosts if they subsequently recover and reproduce. Various plant species were inoculated with four different RNA viruses, Brome mosaic virus (BMV), Cucumber mosaic virus (CMV), Tobacco mosaic virus and Tobacco rattle virus. The inoculated plants were stressed by withholding water. The onset of drought symptoms in virus-infected plants was compared with that in the plants that were inoculated with buffer (mock-inoculated plants). Metabolite profiling analysis was conducted and compared between mock-inoculated and virus-infected plants before and after being subjected to drought stress. In all cases, virus infection delayed the appearance of drought symptoms. Beet plants infected with CMV also exhibited significantly improved tolerance to freezing. Metabolite profiling analysis showed an increase in several osmoprotectants and antioxidants in BMV-infected rice and CMV-infected beet plants before and after drought stress. These results indicate that virus infection improves plant tolerance to abiotic stress, which correlates with increased osmoprotectant and antioxidant levels in infected plants.
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Affiliation(s)
- Ping Xu
- The S. R. Noble Foundation, Ardmore, OK 73401, USA
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