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Fang X, Wu H, Huang W, Ma Z, Jia Y, Min Y, Ma Q, Cai R. The WRKY transcription factor ZmWRKY92 binds to GA synthesis-related genes to regulate maize plant height. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108422. [PMID: 38335889 DOI: 10.1016/j.plaphy.2024.108422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/25/2023] [Accepted: 02/03/2024] [Indexed: 02/12/2024]
Abstract
The plant height is a crucial agronomic trait in contemporary maize breeding. Appropriate plant height can improve crop lodging resistance, increase the planting density and harvest index of crops, and thus contribute to stable and increased yields. In this study, molecular characterization showed that ZmWRKY92 is a nuclear protein and has transcriptional activation in yeast. ZmWRKY92 can specifically bind to the W-box (TTGACC), which was confirmed by double LUC experiments and Yeast one-hybrid assays. Subsequently we screened wrky92 mutants from a library of ethyl methanesulfonate (EMS)-induced mutants. The mutation of a base in ZmWRKY92 leading to the formation of a truncated protein variant is responsible for the dwarfing phenotype of the mutant, which was further verified by allelic testing. Detailed phenotypic analysis revealed that wrky92 mutants have shorter internodes due to reduced internode cell size and lower levels of GA3 and IAA. Transcriptome analysis revealed that the ZmWRKY92 mutation caused significant changes in the expression of genes related to plant height in maize. Additionally, ZmWRKY92 was found to interact with the promoters of ZmGA20ox7 and ZmGID1L2, which are associated with GA synthesis. This study shows that ZmWRKY92 significantly affects the plants height in maize and is crucial in identifying new varieties suitable for growing in high-density conditions.
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Affiliation(s)
- Xiu Fang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hao Wu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wanchang Huang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhongxian Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Jia
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yongwei Min
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Engineering Research Center for Maize of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Engineering Research Center for Maize of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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Ma J, Mudiyanselage SDD, Wang Y. Emerging value of the viroid model in molecular biology and beyond. Virus Res 2022; 313:198730. [PMID: 35263622 PMCID: PMC8976779 DOI: 10.1016/j.virusres.2022.198730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 01/21/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. Research in the past five decades has deciphered the viroid genome structures, viroid replication cycles, numerous host factors for viroid infection, viroid motifs for intracellular and intercellular trafficking, interactions with host defense machinery, etc. In this review, we mainly focus on some significant questions that remain to be tackled, centered around (1) how the RNA polymerase II machinery performs transcription on RNA templates of nuclear-replicating viroids, (2) how viroid RNAs coordinate multiple structural elements for diverse functions, and (3) how viroid RNAs activate plant immunity. Research on viroids has led to seminal discoveries in biology, and we expect the research directions outlined in this review to continue providing key knowledge inspiring other areas of biology.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, MS 39762, USA
| | | | - Ying Wang
- Department of Biological Sciences, Mississippi State University, MS 39762, USA.
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Štajner N, Radišek S, Mishra AK, Nath VS, Matoušek J, Jakše J. Evaluation of Disease Severity and Global Transcriptome Response Induced by Citrus bark cracking viroid, Hop latent viroid, and Their Co-Infection in Hop ( Humulus lupulus L.). Int J Mol Sci 2019; 20:E3154. [PMID: 31261625 PMCID: PMC6651264 DOI: 10.3390/ijms20133154] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/10/2023] Open
Abstract
Viroids are small non-capsidated, single-stranded, covalently-closed circular noncoding RNA replicons of 239-401 nucleotides that exploit host factors for their replication, and some cause disease in several economically important crop plants, while others appear to be benign. The proposed mechanisms of viroid pathogenesis include direct interaction of the genomic viroid RNA with host factors and post-transcriptional or transcriptional gene silencing via viroid-derived small RNAs (vd-sRNAs) generated by the host defensive machinery. Humulus lupulus (hop) plants are hosts to several viroids among which Hop latent viroid (HLVd) and Citrus bark cracking viroid (CBCVd) are attractive model systems for the study of viroid-host interactions due to the symptomless infection of the former and severe symptoms induced by the latter in this indicator host. To better understand their interactions with hop plant, a comparative transcriptomic analysis based on RNA sequencing (RNA-seq) was performed to reveal the transcriptional alterations induced as a result of single HLVd and CBCVd infection in hop. Additionally, the effect of HLVd on the aggressiveness of CBCVd that underlies severe stunting in hop in a mixed infection was studied by transcriptomic analysis. Our analysis revealed that CBCVd infection resulted in dynamic changes in the activity of genes as compared to single HLVd infection and their mixed infection. The differentially expressed genes that are involved in defense, phytohormone signaling, photosynthesis and chloroplasts, RNA regulation, processing and binding; protein metabolism and modification; and other mechanisms were more modulated in the CBCVd infection of hop. Nevertheless, Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in the proteolysis mechanism is more active in a mixed infection as compared to a single one, suggesting co-infecting viroids may result in interference with host factors more prominently. Collectively, our results provide a deep transcriptome of hop and insight into complex single HLVd, CBCVd, and their coinfection in hop-plant interactions.
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Affiliation(s)
- Nataša Štajner
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Plant Protection Department, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Vishnu Sukumari Nath
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jernej Jakše
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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4
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Global Transcriptomic Analysis Reveals Insights into the Response of 'Etrog' Citron ( Citrus medica L.) to Citrus Exocortis Viroid Infection. Viruses 2019; 11:v11050453. [PMID: 31109003 PMCID: PMC6563217 DOI: 10.3390/v11050453] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/11/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022] Open
Abstract
Citrus exocortis viroid (CEVd) is the causal agent of citrus exocortis disease. We employed CEVd-infected ‘Etrog’ citron as a system to study the feedback regulation mechanism using transcriptome analysis in this study. Three months after CEVd infection, the transcriptome of fresh leaves was analyzed, and 1530 differentially expressed genes were detected. The replication of CEVd in citron induced upregulation of genes encoding key proteins that were involved in the RNA silencing pathway such as Dicer-like 2, RNA-dependent RNA polymerase 1, argonaute 2, argonaute 7, and silencing defective 3, as well as those genes encoding proteins that are related to basic defense responses. Many genes involved in secondary metabolite biosynthesis and chitinase activity were upregulated, whereas other genes related to cell wall and phytohormone signal transduction were downregulated. Moreover, genes encoding disease resistance proteins, pathogenicity-related proteins, and heat shock cognate 70 kDa proteins were also upregulated in response to CEVd infection. These results suggest that basic defense and RNA silencing mechanisms are activated by CEVd infection, and this information improves our understanding of the pathogenesis of viroids in woody plants.
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Aviña-Padilla K, Rivera-Bustamante R, Kovalskaya NY, Hammond RW. Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development. Viruses 2018; 10:v10100516. [PMID: 30241423 PMCID: PMC6213050 DOI: 10.3390/v10100516] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022] Open
Abstract
Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and number of fruits, resulting in significant crop losses. Dramatic alterations in plant development triggered by viroid infection are the result of differential gene expression; in our study, we focused on the effect of tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) infection on gene networks associated with the regulation of flower and fruit development. The expression of several of the genes were previously reported to be affected by viroid infection, but two genes not previously studied were included. Changes in gene expression of SlBIGPETAL1 (bHLH transcription factor) and SlOVA6 (proline-like tRNA synthetase) are involved in petal morphology and fertility, respectively. Expression of SlOVA6 was down-regulated in flowers of TPMVd- and MPVd-infected plants, while expression of SlBIGPETAL1 was up-regulated in flowers. Up-regulation of SlBIGPETAL1 and down-regulation of SlOVA6 were positively correlated with symptoms such as reduced petal size and flower abortion. Expression analysis of additional tomato genes and a prediction of a global network association of genes involved in flower and fruit development and impacted by viroid infection may further elucidate the pathways underlying viroid pathogenicity.
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Affiliation(s)
- Katia Aviña-Padilla
- Campus Juriquilla, Universidad Nacional Autónoma de Mexico, Querátaro Qro 76300, Mexico.
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato 36821, Mexico.
| | - Rafael Rivera-Bustamante
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato 36821, Mexico.
| | - Natalia Y Kovalskaya
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
| | - Rosemarie W Hammond
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
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6
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Więsyk A, Iwanicka-Nowicka R, Fogtman A, Zagórski-Ostoja W, Góra-Sochacka A. Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid. Viruses 2018; 10:v10050257. [PMID: 29762480 PMCID: PMC5977250 DOI: 10.3390/v10050257] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 01/06/2023] Open
Abstract
Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in “Rutgers” tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage; (ii) early symptoms; (iii) full spectrum of symptoms and (iv) the so-called ‘recovery’ stage, when stem regrowth was observed in severely affected plants. Gene expression profiles differed depending on stage of infection and variant. In S23-infected plants, the expression of over 3000 genes was affected, while M-infected plants showed 3-fold fewer differentially expressed genes, only 20% of which were specific to the M variant. The differentially expressed genes included many genes related to stress; defense; hormone metabolism and signaling; photosynthesis and chloroplasts; cell wall; RNA regulation, processing and binding; protein metabolism and modification and others. The expression levels of several genes were confirmed by nCounter analysis.
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Affiliation(s)
- Aneta Więsyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
| | - Roksana Iwanicka-Nowicka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
| | - Włodzimierz Zagórski-Ostoja
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
| | - Anna Góra-Sochacka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
- Correspondence: ; Tel.: +48-22-592-34-08; Fax: +48-22-592-21-90
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7
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Xia C, Li S, Hou W, Fan Z, Xiao H, Lu M, Sano T, Zhang Z. Global Transcriptomic Changes Induced by Infection of Cucumber ( Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid. Front Microbiol 2017; 8:2427. [PMID: 29312160 PMCID: PMC5733102 DOI: 10.3389/fmicb.2017.02427] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/23/2017] [Indexed: 11/13/2022] Open
Abstract
Fifteen years after transfer to hops, hop stunt viroid-grapevine (HSVd-g) was replaced by HSVd-hop (HSVd-h), a sequence variant that contains changes at five different positions. HSVd-g54 is a laboratory mutant derived from HSVd-g that differs from its progenitor by a single G to A substitution at position 54. While infection by HSVd-h induces only mild stunting in cucumber (Cucumis sativus L.), HSVd-g54 induces much more severe symptoms in this indicator host. Comparison of transcriptome profiles of cucumber infected with HSVd-h or HSVd-g54 with those of mock-inoculated controls obtained by whole transcriptome shotgun sequencing revealed that many genes related to photosynthesis were down-regulated following infection. In contrast, genes encoding RNA-dependent RNA polymerase 1 (CsRDR1), especially CsRDR1c1 and CsRDR1c2, as well as those related to basal defense responses were up-regulated. Expression of genes associated with phytohormone signaling pathways were also altered, indicating that viroid infection initiates a complex array of changes in the host transcriptome. HSVd-g54 induced an earlier and stronger response than HSVd-h, and further examination of these differences will contribute to a better understanding of the mechanisms that determine viroid pathogenicity.
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Affiliation(s)
- Changjian Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, State Tobacco Monopoly Bureau, Institue of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hong Xiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiguang Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Zhixiang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Kappagantu M, Bullock JM, Nelson ME, Eastwell KC. Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:842-851. [PMID: 28703029 DOI: 10.1094/mpmi-03-17-0071-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viroids are the smallest known plant pathogens that exploit host systems for their replication and cause diseases in many hosts. In this study, the host response of hop plants to Hop stunt viroid (HSVd) infection was studied through transcriptome analysis. RNA sequence analysis of hop leaves infected with HSVd revealed dynamic changes in hop gene expression. Defense-related genes and genes involved in lipid and terpenoid metabolism are the major categories that showed differential expression due to HSVd infection. Additionally, the effect of HSVd on development of hop powdery mildew (Podospheara macularis) (HPM) was studied. Transcriptome analysis followed by quantitative reverse transcription-polymerase chain reaction analysis showed that transcript levels of pathogenesis-related (PR) genes such as PR protein 1, chitinase, and thaumatin-like protein genes are induced in leaves infected with HPM alone. The response in these genes to HPM is significantly down-regulated in leaves with HSVd-HPM mixed infection. These results confirm that HSVd alters host metabolism, physiology, and plant defense responses. Nevertheless, in detached leaf assays, HPM consistently expanded faster on HSVd-negative leaves relative to HSVd-positive leaves. Although HSVd infection suppresses elements associated with the host immunity response, infection by HSVd is antagonistic to HPM infection of hops.
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Affiliation(s)
- Madhu Kappagantu
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Jeff M Bullock
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Mark E Nelson
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Kenneth C Eastwell
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
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Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans-Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses. J Virol 2017; 91:JVI.00247-17. [PMID: 28331096 DOI: 10.1128/jvi.00247-17] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 03/16/2017] [Indexed: 11/20/2022] Open
Abstract
Many pathogens express noncoding RNAs (ncRNAs) during infection processes. In the most extreme case, pathogenic ncRNAs alone (such as viroids) can infect eukaryotic organisms, leading to diseases. While a few pathogenic ncRNAs have been implicated in regulating gene expression, the functions of most pathogenic ncRNAs in host-pathogen interactions remain unclear. Here, we employ potato spindle tuber viroid (PSTVd) infecting tomato as a system to dissect host interactions with pathogenic ncRNAs, using comprehensive transcriptome analyses. We uncover various new activities in regulating gene expression during PSTVd infection, such as genome-wide alteration in alternative splicing of host protein-coding genes, enhanced guided-cleavage activities of a host microRNA, and induction of the trans-acting function of phased secondary small interfering RNAs. Furthermore, we reveal that PSTVd infection massively activates genes involved in plant immune responses, mainly those in the calcium-dependent protein kinase and mitogen-activated protein kinase cascades, as well as prominent genes involved in hypersensitive responses, cell wall fortification, and hormone signaling. Intriguingly, our data support a notion that plant immune systems can respond to pathogenic ncRNAs, which has broad implications for providing new opportunities for understanding the complexity of immune systems in differentiating "self" and "nonself," as well as lay the foundation for resolving the long-standing question regarding the pathogenesis mechanisms of viroids and perhaps other infectious RNAs.IMPORTANCE Numerous pathogens, including viruses, express pathogenic noncoding transcripts during infection. In the most extreme case, pathogenic noncoding RNAs alone (i.e., viroids) can cause disease in plants. While some work has demonstrated that pathogenic noncoding RNAs interact with host factors for function, the biological significance of pathogenic noncoding RNAs in host-pathogen interactions remains largely unclear. Here, we apply comprehensive genome-wide analyses of plant-viroid interactions and discover several novel molecular activities underlying nuclear-replicating viroid infection processes in plants, including effects on the expression and function of host noncoding transcripts, as well as the alternative splicing of host protein-coding genes. Importantly, we show that plant immunity is activated upon infection of a nuclear-replicating viroid, which is a new concept that helps to understand viroid-based pathogenesis. Our finding has broad implications for understanding the complexity of host immune systems and the diverse functions of noncoding RNAs.
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Avina-Padilla K, Martinez de la Vega O, Rivera-Bustamante R, Martinez-Soriano JP, Owens RA, Hammond RW, Vielle-Calzada JP. In silico prediction and validation of potential gene targets for pospiviroid-derived small RNAs during tomato infection. Gene 2015; 564:197-205. [DOI: 10.1016/j.gene.2015.03.076] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/13/2015] [Accepted: 03/24/2015] [Indexed: 12/31/2022]
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11
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What has been happening with viroids? Virus Genes 2014; 49:175-84. [DOI: 10.1007/s11262-014-1110-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/18/2014] [Indexed: 12/18/2022]
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Abstract
Viroids are the smallest autonomous infectious nucleic acids known today. They are non-coding, unencapsidated, circular RNAs with sizes ranging from 250 to 400 nucleotides and infect certain plants. These RNAs are transcribed by rolling-circle mechanisms in the plant host's nuclei (Pospiviroidae) or chloroplasts (Avsunviroidae). Since viroids lack any open reading frame, their pathogenicity has for a long time been a conundrum. Recent findings, however, show that viroid infection is associated with the appearance of viroid-specific small RNA (vsRNA). These have sizes similar to endogenous small interfering RNA and microRNA and thus might alter the normal gene expression in the host plant. In this review we will summarize the current knowledge on vsRNA and discuss the current hypotheses how they connect to the induced symptoms, which vary dramatically, depending on both the plant cultivar and the viroid strain.
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Affiliation(s)
- Christian Hammann
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Darmstadt, Germany.
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13
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Owens RA, Tech KB, Shao JY, Sano T, Baker CJ. Global analysis of tomato gene expression during Potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:582-98. [PMID: 22217247 DOI: 10.1094/mpmi-09-11-0258] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Viroids like Potato spindle tuber viroid (PSTVd) are the smallest known agents of infectious disease-small, highly structured, circular RNA molecules that lack detectable messenger RNA activity, yet are able to replicate autonomously in susceptible plant species. To better understand the possible role of RNA silencing in disease induction, a combination of microarray analysis and large-scale RNA sequence analysis was used to compare changes in tomato gene expression and microRNA levels associated with PSTVd infection in two tomato cultivars plus a third transformed line expressing small PSTVd small interfering RNAs in the absence of viroid replication. Changes in messenger (m)RNA levels for the sensitive cultivar 'Rutgers' were extensive, involving more than half of the approximately 10,000 genes present on the array. Chloroplast biogenesis was down-regulated in both sensitive and tolerant cultivars, and effects on mRNAs encoding enzymes involved in the biosynthesis of gibberellin and other hormones were accompanied by numerous changes affecting their respective signaling pathways. In the dwarf cultivar 'MicroTom', a marked upregulation of genes involved in response to stress and other stimuli was observed only when exogenous brassinosteroid was applied to infected plants, thereby providing the first evidence for the involvement of brassinosteroid-mediated signaling in viroid disease induction.
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Affiliation(s)
- Robert A Owens
- Molecular Plant Pathology Laboratory (USDA/ARS), 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
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14
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Wang Y, Shibuya M, Taneda A, Kurauchi T, Senda M, Owens RA, Sano T. Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars. Virology 2011; 413:72-83. [PMID: 21353278 DOI: 10.1016/j.virol.2011.01.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/07/2010] [Accepted: 01/14/2011] [Indexed: 12/31/2022]
Abstract
To better understand the biogenesis of viroid-specific small RNAs and their possible role in disease induction, we have examined the accumulation of these small RNAs in potato spindle tuber viroid (PSTVd)-infected tomato plants. Large-scale sequence analysis of viroid-specific small RNAs revealed active production from the upper portion of the pathogenicity and central domains, two regions previously thought to be underrepresented. Profiles of small RNA populations derived from PSTVd antigenomic RNA were more variable, with differences between infected Rutgers (severe symptoms) and Moneymaker (mild symptoms) plants pointing to possible cultivar-specific differences in small RNA synthesis and/or stability. Using microarray analysis, we monitored the effects of PSTVd infection on the expression levels of >100 tomato genes containing potential binding sites for PSTVd small RNAs. Of 18 such genes down-regulated early in infection, two genes involved in gibberellin or jasmonic acid biosynthesis contain binding sites for PSTVd small RNAs in their respective ORFs.
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Affiliation(s)
- Ying Wang
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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Owens RA, Hammond RW. Viroid pathogenicity: one process, many faces. Viruses 2009; 1:298-316. [PMID: 21994551 PMCID: PMC3185495 DOI: 10.3390/v1020298] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 12/28/2022] Open
Abstract
Despite the non-coding nature of their small RNA genomes, the visible symptoms of viroid infection resemble those associated with many plant virus diseases. Recent evidence indicates that viroid-derived small RNAs acting through host RNA silencing pathways play a key role in viroid pathogenicity. Host responses to viroid infection are complex, involving signaling cascades containing host-encoded protein kinases and crosstalk between hormonal and defense-signaling pathways. Studies of viroid-host interaction in the context of entire biochemical or developmental pathways are just beginning, and many working hypotheses have yet to be critically tested.
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Affiliation(s)
- Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA; E-mail:
| | - Rosemarie W. Hammond
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA; E-mail:
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