151
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Abstract
Some DNA viruses overcome plant defenses by producing a suppressor protein that blocks the silencing of viral genes.
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Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (IAL), Universidad Nacional del Litoral-CONICET, Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (IAL), Universidad Nacional del Litoral-CONICET, Santa Fe, Argentina
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152
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Bengyella L, Waikhom SD, Allie F, Rey C. Virus tolerance and recovery from viral induced-symptoms in plants are associated with transcriptome reprograming. PLANT MOLECULAR BIOLOGY 2015; 89:243-52. [PMID: 26358043 DOI: 10.1007/s11103-015-0362-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/08/2015] [Indexed: 05/07/2023]
Abstract
Plant recovery from viral infection is characterized by initial severe systemic symptoms which progressively decrease, leading to reduced symptoms or symptomless leaves at the apices. A key feature to plant recovery from invading nucleic acids such as viruses is the degree of the host's initial basal immunity response. We review current links between RNA silencing, recovery and tolerance, and present a model in which, in addition to regulation of resistance (R) and other defence-related genes by RNA silencing, viral infections incite perturbations of the host physiological state that trigger reprogramming of host responses to by-pass severe symptom development, leading to partial or complete recovery. Recovery, in particular in perennial hosts, may trigger tolerance or virus accommodation. We discuss evidence suggesting that plant viruses can avoid total clearance but persistently replicate at low levels, thereby modulating the host transcriptome response which minimizes fitness cost and triggers recovery from viral-symptoms. In some cases a susceptible host may fail to recover from initial viral systemic symptoms, yet, accommodates the persistent virus throughout the life span, a phenomenon herein referred to as non-recovery accommodation, which differs from tolerance in that there is no distinct recovery phase, and differs from susceptibility in that the host is not killed. Recent advances in plant recovery from virus-induced symptoms involving host transcriptome reprogramming are discussed.
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Affiliation(s)
- Louis Bengyella
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts 6, Ave, Johannesburg, Braamfontein, 2000, South Africa
| | - Sayanika D Waikhom
- Centre of Advanced Study in Life Sciences, Manipur University, Imphal, Manipur, 795003, India
- School of Basic and Biomedical Science, University of Health and Allied Sciences, PMB 31, Ho, Volta Region, Ghana
| | - Farhahna Allie
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts 6, Ave, Johannesburg, Braamfontein, 2000, South Africa
| | - Chrissie Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts 6, Ave, Johannesburg, Braamfontein, 2000, South Africa.
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153
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Li F, Xu X, Huang C, Gu Z, Cao L, Hu T, Ding M, Li Z, Zhou X. The AC5 protein encoded by Mungbean yellow mosaic India virus is a pathogenicity determinant that suppresses RNA silencing-based antiviral defenses. THE NEW PHYTOLOGIST 2015; 208:555-69. [PMID: 26010321 DOI: 10.1111/nph.13473] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
It is generally accepted that begomoviruses in the family Geminiviridae encode four proteins (from AC1/C1 to AC4/C4) using the complementary-sense DNA as template. Although AC5/C5 coding sequences are increasingly annotated in databases for many begomoviruses, the evolutionary relationships and functions of this putative protein in viral infection are obscure. Here, we demonstrate several important functions of the AC5 protein of a bipartite begomovirus, Mungbean yellow mosaic India virus (MYMIV). Mutational analyses and transgenic expression showed that AC5 plays a critical role in MYMIV infection. Ectopic expression of AC5 from a Potato virus X (PVX) vector resulted in severe mosaic symptoms followed by a hypersensitive-like response in Nicotiana benthamiana. Furthermore, MYMIV AC5 effectively suppressed post-transcriptional gene silencing induced by single-stranded but not double-stranded RNA. AC5 was also able to reverse transcriptional gene silencing of a green fluorescent protein transgene by reducing methylation of promoter sequences, probably through repressing expression of a CHH cytosine methyltransferase (DOMAINS REARRANGED METHYLTRANSFERASE2) in N. benthamiana. Our results demonstrate that MYMIV AC5 is a pathogenicity determinant and a potent RNA silencing suppressor that employs novel mechanisms to suppress antiviral defenses, and suggest that the AC5 function may be conserved among many begomoviruses.
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Affiliation(s)
- Fangfang Li
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiongbiao Xu
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Changjun Huang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zhouhang Gu
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Linge Cao
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ming Ding
- Institute of Plant Protection, Yunnan Provincial Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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154
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Carbonell A, Carrington JC. Antiviral roles of plant ARGONAUTES. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:111-7. [PMID: 26190744 PMCID: PMC4618181 DOI: 10.1016/j.pbi.2015.06.013] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/11/2015] [Accepted: 06/19/2015] [Indexed: 05/20/2023]
Abstract
ARGONAUTES (AGOs) are the effector proteins functioning in eukaryotic RNA silencing pathways. AGOs associate with small RNAs and are programmed to target complementary RNA or DNA. Plant viruses induce a potent and specific antiviral RNA silencing host response in which AGOs play a central role. Antiviral AGOs associate with virus-derived small RNAs to repress complementary viral RNAs or DNAs, or with endogenous small RNAs to regulate host gene expression and promote antiviral defense. Here, we review recent progress towards understanding the roles of plant AGOs in antiviral defense. We also discuss the strategies that viruses have evolved to modulate, attenuate or suppress AGO antiviral functions.
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Affiliation(s)
- Alberto Carbonell
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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155
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Castillo-González C, Liu X, Huang C, Zhao C, Ma Z, Hu T, Sun F, Zhou Y, Zhou X, Wang XJ, Zhang X. Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense. eLife 2015; 4:e06671. [PMID: 26344546 PMCID: PMC4606454 DOI: 10.7554/elife.06671] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 09/05/2015] [Indexed: 12/15/2022] Open
Abstract
Transcriptional gene silencing (TGS) can serve as an innate immunity against invading DNA viruses throughout Eukaryotes. Geminivirus code for TrAP protein to suppress the TGS pathway. Here, we identified an Arabidopsis H3K9me2 histone methyltransferase, Su(var)3-9 homolog 4/Kryptonite (SUVH4/KYP), as a bona fide cellular target of TrAP. TrAP interacts with the catalytic domain of KYP and inhibits its activity in vitro. TrAP elicits developmental anomalies phenocopying several TGS mutants, reduces the repressive H3K9me2 mark and CHH DNA methylation, and reactivates numerous endogenous KYP-repressed loci in vivo. Moreover, KYP binds to the viral chromatin and controls its methylation to combat virus infection. Notably, kyp mutants support systemic infection of TrAP-deficient Geminivirus. We conclude that TrAP attenuates the TGS of the viral chromatin by inhibiting KYP activity to evade host surveillance. These findings provide new insight on the molecular arms race between host antiviral defense and virus counter defense at an epigenetic level. DOI:http://dx.doi.org/10.7554/eLife.06671.001 Many viruses can infect plants and cause diseases that can reduce crop yields. The Geminiviruses are a family of plant viruses that are transmitted by insects and infect tomato, cabbage, and many other crop plants. These viruses hijack the plant cells that they infect and force the plant cells to make viral proteins using instructions provided by the genes in the virus' own DNA. To make proteins, DNA is first copied into molecules of messenger ribonucleic acid (or mRNA) in a process called transcription. However, plants can defend themselves by blocking the transcription of viral DNA through ‘transcriptional gene silencing’. In plant cells, DNA is packaged around proteins called histones to form a structure called chromatin. Small chemical tags attached to the histones can alter the structure of chromatin to regulate the activity of the genes encoded within it. For example, ‘methyl’ tags added to certain histones can block transcription and lower the activity of a gene. DNA from viruses can also associate with histones inside plant cells meaning that transcriptional gene silencing can take place by the addition of these methyl tags. Many Geminiviruses produce a protein called TrAP, which can activate transcription, but it is not clear how this works. Castillo-González et al. studied the TrAP proteins from two different Geminiviruses that can infect crop plants. The commonly used model plant, Arabidopsis thaliana, was genetically engineered to produce high levels of these TrAP proteins. These ‘transgenic’ plants did not develop properly: they grew more slowly, had abnormal leaves, and flowered earlier. Furthermore, hundreds of plant genes were more active than usual in the transgenic plants, which suggests that TrAP inhibits transcriptional gene silencing. Further experiments showed that TrAP directly binds to a plant enzyme called KYP—which normally deposits methyl groups on chromatin and prevents it from working. This reduces the number of methyl groups that are attached to histones associated with both viral and plant chromatin, which results in the activation of genes that would normally be switched off. Castillo-González et al.'s findings show how Geminiviruses can stop transcriptional gene silencing of chromatin that contains virus DNA to evade the host plant's defenses. The next challenge is to understand how TrAP inhibits KYP, which may present new ways to genetically engineer plants to become resistant to infection by viruses. DOI:http://dx.doi.org/10.7554/eLife.06671.002
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Affiliation(s)
- Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
| | - Xiuying Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Changjun Huang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States.,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Yunnan Academy of Tobacco Agricultural Sciences, Yunnan, China
| | - Changjiang Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States.,College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
| | - Tao Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States.,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States.,Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xueping Zhou
- Biotechnology Institute, College of Agriculture & Biotechnology, Zhejiang University, Zhejiang, China
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
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156
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Patil BL, Fauquet CM. Light intensity and temperature affect systemic spread of silencing signal in transient agroinfiltration studies. MOLECULAR PLANT PATHOLOGY 2015; 16:484-94. [PMID: 25220764 PMCID: PMC6638542 DOI: 10.1111/mpp.12205] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
RNA silencing is a sequence-specific post-transcriptional gene inactivation mechanism that operates in diverse organisms and that can extend beyond its site of initiation, owing to the movement of the silencing signal, called non-autonomous gene silencing. Previous studies have shown that several factors manifest the movement of the silencing signal, such as the size (21 or 24 nucleotides) of the secondary small interfering RNA (siRNA) produced, the steady-state concentration of siRNAs and their cognate messenger RNA (mRNA) or a change in the sink-source status of plant parts affecting phloem translocation. Our study shows that both light intensity and temperature have a significant impact on the systemic movement of the silencing signal in transient agroinfiltration studies in Nicotiana benthamiana. At higher light intensities (≥ 450 μE/m(2)/s) and higher temperatures (≥ 30 °C), gene silencing was localized to leaf tissue that was infiltrated, without any systemic spread. Interestingly, in these light and temperature conditions (≥ 450 μE/m(2) /s and ≥ 30 °C), the N. benthamiana plants showed recovery from the viral symptoms. However, the reduced systemic silencing and reduced viral symptom severity at higher light intensities were caused by a change in the sink-source status of the plant, ultimately affecting the phloem translocation of small RNAs or the viral genome. In contrast, at lower light intensities (<300 μE/m(2)/s) with a constant temperature of 25 °C, there was strong systemic movement of the silencing signal in the N. benthamiana plants and reduced recovery from virus infections. The accumulation of gene-specific siRNAs was reduced at higher temperature as a result of a reduction in the accumulation of transcript on transient agroinfiltration of RNA interference (RNAi) constructs, mostly because of poor T-DNA transfer activity of Agrobacterium, possibly also accompanied by reduced phloem translocation.
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Affiliation(s)
- Basavaprabhu L Patil
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO, 63132, USA; National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, 110012, India
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157
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Patil BL, Fauquet CM. Studies on differential behavior of cassava mosaic geminivirus DNA components, symptom recovery patterns, and their siRNA profiles. Virus Genes 2015; 50:474-86. [PMID: 25724177 DOI: 10.1007/s11262-015-1184-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/18/2015] [Indexed: 11/28/2022]
Abstract
Cassava mosaic disease caused by cassava mosaic geminiviruses (CMGs) with bipartite genome organization is a major constraint for production of cassava in the African continent and the Indian sub-continent. Currently, there are eleven recognized species of CMGs, and several diverse isolates represent them, with vast amount of sequence variability, reflecting into diversity of symptom severity/phenotypes. Here, we make a systematic effort to study the infection dynamics of several species of CMGs and their isolates. Further, we try to identify the genomic component of CMGs contributing to the manifestation of diverse patterns of symptoms and the molecular basis for the differential behavior of CMGs. The pseudo-recombination studies carried out by swapping of DNA-A and DNA-B components of the CMGs revealed that the DNA-B component significantly contributes to the symptom severity. Past studies had shown that the DNA-A component of Sri Lankan cassava mosaic virus shows monopartite feature. Thus, the ability of DNA-A component alone, to replicate and move systemically in the host plant with inherent monopartite features was investigated for all the CMGs. Geminiviruses are known to trigger gene silencing and are also its target, resulting in recovery of the host plant from viral infection. In the collection of several different CMG species and isolates we had, there was a vast variability in their recovery and non-recovery phenotypes. To understand the molecular basis of this, the origin and distribution of virus-derived small interfering RNAs were mapped across their genome and across the CMG-infected symptomatic Nicotiana benthamiana.
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158
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Involvement of host regulatory pathways during geminivirus infection: a novel platform for generating durable resistance. Funct Integr Genomics 2015; 14:47-58. [PMID: 24233104 DOI: 10.1007/s10142-013-0346-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/04/2013] [Accepted: 10/21/2013] [Indexed: 12/20/2022]
Abstract
Geminiviruses are widely distributed throughout the world and cause devastating yield losses in almost all the economically important crops. In this review, the newly identified roles of various novel plant factors and pathways participating in plant–virus interaction are summarized with a particular focus on the exploitation of various pathways involving ubiquitin/26S proteasome pathway, small RNA pathways, cell division cycle components, and the epigenetic mechanism as defense responses during plant–pathogen interactions. Capturing the information on these pathways for the development of strategies against geminivirus infection is argued to provide the basis for new genetic approaches to resistance.
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159
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Xie M, Yu B. siRNA-directed DNA Methylation in Plants. Curr Genomics 2015; 16:23-31. [PMID: 25937811 PMCID: PMC4412961 DOI: 10.2174/1389202915666141128002211] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 12/02/2022] Open
Abstract
DNA cytosine methylationis an important epigenetic process that is correlated with transgene silencing, transposon suppression, and gene imprinting. In plants, small interfering RNAs (siRNAs) can trigger DNA methylation at loci containing their homolog sequences through a process called RNA-directed DNA methylation (RdDM). In canonical RdDM, 24 nucleotide (nt) siRNAs (ra-siRNAs) will be loaded into their effector protein called ARGONAUTE 4 (AGO4) and subsequently targeted to RdDM loci through base-pairing with the non-coding transcripts produced by DNA-directed RNA Polymerase V. Then, the AGO4-ra-siRNA will recruit the DNA methyltransferase to catalyze de novo DNA methylation. Recent studies also identified non-canonical RdDM pathways that involve microRNAs or 21 nt siRNAs. These RdDM pathways are biologically important since they control responses biotic and abiotic stresses, maintain genome stability and regulate development. Here, we summarize recent pro-gresses of mechanisms governing canonical and non-canonical RdDM pathways.
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Affiliation(s)
- Meng Xie
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0660, USA
| | - Bin Yu
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0660, USA
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160
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Symptom recovery in virus-infected plants: Revisiting the role of RNA silencing mechanisms. Virology 2015; 479-480:167-79. [DOI: 10.1016/j.virol.2015.01.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/02/2015] [Accepted: 01/08/2015] [Indexed: 01/11/2023]
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161
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Csorba T, Kontra L, Burgyán J. viral silencing suppressors: Tools forged to fine-tune host-pathogen coexistence. Virology 2015; 479-480:85-103. [DOI: 10.1016/j.virol.2015.02.028] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/31/2015] [Accepted: 02/16/2015] [Indexed: 12/27/2022]
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162
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Maredza AT, Allie F, Plata G, Rey MEC. Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection. Mol Genet Genomics 2015; 291:1467-85. [PMID: 25920485 DOI: 10.1007/s00438-015-1049-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
Abstract
Cassava is an important food security crop in Sub-Saharan Africa. Two episomal begomovirus-associated sequences, named Sequences Enhancing Geminivirus Symptoms (SEGS1 and SEGS2), were identified in field cassava affected by the devastating cassava mosaic disease (CMD). The sequences reportedly exacerbated CMD symptoms in the tolerant cassava landrace TME3, and the model plants Arabidopsis thaliana and Nicotiana benthamiana, when biolistically co-inoculated with African cassava mosaic virus-Cameroon (ACMV-CM) or East African cassava mosaic virus-UG2 (EACMV-UG2). Following the identification of small SEGS fragments in the cassava EST database, the intention of this study was to confirm their presence in the genome, and investigate a possible role for these sequences in CMD. We report that multiple copies of varying lengths of both SEGS1 and SEGS2 are widely distributed in the sequenced cassava genome and are present in several other cassava accessions screened by PCR. The endogenous SEGS1 and SEGS2 are in close proximity or overlapping with cassava genes, suggesting a possible role in regulation of specific biological processes. We confirm the expression of SEGS in planta using EST data and RT-PCR. The sequence features of endogenous SEGS (iSEGS) are unique but resemble non-autonomous transposable elements (TEs) such as MITEs and helitrons. Furthermore, many SEGS-associated genes, some involved in virus-host interactions, are differentially expressed in susceptible (T200) and tolerant TME3) cassava landraces infected by South African cassava mosaic virus (SACMV) of susceptible (T200) and tolerant (TME3) cassava landraces. Abundant SEGS-derived small RNAs were also present in mock-inoculated and SACMV-infected T200 and TME3 leaves. Given the known role of TEs and associated genes in gene regulation and plant immune responses, our observations are consistent with a role of these DNA elements in the host's regulatory response to geminiviruses.
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Affiliation(s)
- A T Maredza
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa
| | - F Allie
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa
| | - G Plata
- Department of Systems Biology, Columbia University in the City of New York, 1130 St Nicholas Avenue, New York, NY, USA
| | - M E C Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa.
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163
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Nygren J, Shad N, Kvarnheden A, Westerbergh A. Variation in susceptibility to Wheat dwarf virus among wild and domesticated wheat. PLoS One 2015; 10:e0121580. [PMID: 25837893 PMCID: PMC4383415 DOI: 10.1371/journal.pone.0121580] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 02/13/2015] [Indexed: 01/06/2023] Open
Abstract
We investigated the variation in plant response in host-pathogen interactions between wild (Aegilops spp., Triticum spp.) and domesticated wheat (Triticum spp.) and Wheat dwarf virus (WDV). The distribution of WDV and its wild host species overlaps in Western Asia in the Fertile Crescent, suggesting a coevolutionary relationship. Bread wheat originates from a natural hybridization between wild emmer wheat (carrying the A and B genomes) and the wild D genome donor Aegilops tauschii, followed by polyploidization and domestication. We studied whether the strong selection during these evolutionary processes, leading to genetic bottlenecks, may have resulted in a loss of resistance in domesticated wheat. In addition, we investigated whether putative fluctuations in intensity of selection imposed on the host-pathogen interactions have resulted in a variation in susceptibility to WDV. To test our hypotheses we evaluated eighteen wild and domesticated wheat taxa, directly or indirectly involved in wheat evolution, for traits associated with WDV disease such as leaf chlorosis, different growth traits and WDV content. The plants were exposed to viruliferous leafhoppers (Psammotettix alienus) in a greenhouse trial and evaluated at two time points. We found three different plant response patterns: i) continuous reduction in growth over time, ii) weak response at an early stage of plant development but a much stronger response at a later stage, and iii) remission of symptoms over time. Variation in susceptibility may be explained by differences in the intensity of natural selection, shaping the coevolutionary interaction between WDV and the wild relatives. However, genetic bottlenecks during wheat evolution have not had a strong impact on WDV resistance. Further, this study indicates that the variation in susceptibility may be associated with the genome type and that the ancestor Ae. tauschii may be useful as genetic resource for the improvement of WDV resistance in wheat.
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Affiliation(s)
- Jim Nygren
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nadeem Shad
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Kvarnheden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
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164
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Saeed M, Krczal G, Wassenegger M. Three gene products of a begomovirus-betasatellite complex restore expression of a transcriptionally silenced green fluorescent protein transgene in Nicotiana benthamiana. Virus Genes 2015; 50:340-4. [PMID: 25537949 DOI: 10.1007/s11262-014-1155-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/04/2014] [Indexed: 11/30/2022]
Abstract
Single-stranded DNA geminiviruses replicate via double-stranded DNA intermediates forming mini-chromosomes that are targets for transcriptional gene silencing (TGS) in plants. The ability of the cotton leaf curl Kokhran virus (CLCuKoV)-cotton leaf curl Multan betasatellite (CLCuMuB) proteins, replication-associated protein (Rep), transcriptional activator protein (TrAP), C4, V2 and βC1, to suppress TGS was investigated by using the Nicotiana benthamiana line 16-TGS (16-TGS) harbouring a transcriptionally silenced green fluorescent protein (GFP) transgene. Inoculation of 16-TGS plants with a recombinant potato virus X vector carrying Rep, TrAP or βC1 resulted in re-expression of GFP. Northern blot analysis confirmed that the observed GFP fluorescence was associated with GFP mRNA accumulation. These results indicated that Rep, TrAP and βC1 proteins of CLCuKoV-CLCuMuB can re-activate the expression of a transcriptionally silenced GFP transgene in N. benthamiana. Although Rep, TrAP, or βC1 proteins have, for other begomoviruses or begomoviruses-betasatellites, been previously shown to have TGS suppressor activity, this is the first report demonstrating that a single begomovirus-betasatellite complex encodes three suppressors of TGS.
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Affiliation(s)
- Muhammad Saeed
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, 67435, Neustadt, Germany,
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165
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Jackel JN, Buchmann RC, Singhal U, Bisaro DM. Analysis of geminivirus AL2 and L2 proteins reveals a novel AL2 silencing suppressor activity. J Virol 2015. [PMID: 25552721 DOI: 10.1128/jvi.02625-2614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
UNLABELLED Both posttranscriptional and transcriptional gene silencing (PTGS and TGS, respectively) participate in defense against the DNA-containing geminiviruses. As a countermeasure, members of the genus Begomovirus (e.g., Cabbage leaf curl virus) encode an AL2 protein that is both a transcriptional activator and a silencing suppressor. The related L2 protein of Beet curly top virus (genus Curtovirus) lacks transcription activation activity. Previous studies showed that both AL2 and L2 suppress silencing by a mechanism that correlates with adenosine kinase (ADK) inhibition, while AL2 in addition activates transcription of cellular genes that negatively regulate silencing pathways. The goal of this study was to clarify the general means by which these viral proteins inhibit various aspects of silencing. We confirmed that AL2 inhibits systemic silencing spread by a mechanism that requires transcription activation activity. Surprisingly, we also found that reversal of PTGS and TGS by ADK inactivation depended on whether experiments were conducted in vegetative or reproductive Nicotiana benthamiana plants (i.e., before or after the vegetative-to-reproductive transition). While AL2 was able to reverse silencing in both vegetative and reproductive plants, L2 and ADK inhibition were effective only in vegetative plants. This suggests that silencing maintenance mechanisms can change during development or in response to stress. Remarkably, we also observed that AL2 lacking its transcription activation domain could reverse TGS in reproductive plants, revealing a third, previously unsuspected AL2 suppression mechanism that depends on neither ADK inactivation nor transcription activation. IMPORTANCE RNA silencing in plants is a multivalent antiviral defense, and viruses respond by elaborating multiple and sometimes multifunctional proteins that inhibit various aspects of silencing. The studies described here add an additional layer of complexity to this interplay. By examining geminivirus AL2 and L2 suppressor activities, we show that L2 is unable to suppress silencing in Nicotiana benthamiana plants that have undergone the vegetative-to-reproductive transition. As L2 was previously shown to be effective in mature Arabidopsis plants, these results illustrate that silencing mechanisms can change during development or in response to stress in ways that may be species specific. The AL2 and L2 proteins are known to share a suppression mechanism that correlates with the ability of both proteins to inhibit ADK, while AL2 in addition can inhibit silencing by transcriptionally activating cellular genes. Here, we also provide evidence for a third AL2 suppression mechanism that depends on neither transcription activation nor ADK inactivation. In addition to revealing the remarkable versatility of AL2, this work highlights the utility of viral suppressors as probes for the analysis of silencing pathways.
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Affiliation(s)
- Jamie N Jackel
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - R Cody Buchmann
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - Udit Singhal
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
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166
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Jackel JN, Buchmann RC, Singhal U, Bisaro DM. Analysis of geminivirus AL2 and L2 proteins reveals a novel AL2 silencing suppressor activity. J Virol 2015; 89:3176-87. [PMID: 25552721 PMCID: PMC4337558 DOI: 10.1128/jvi.02625-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/26/2014] [Indexed: 01/02/2023] Open
Abstract
UNLABELLED Both posttranscriptional and transcriptional gene silencing (PTGS and TGS, respectively) participate in defense against the DNA-containing geminiviruses. As a countermeasure, members of the genus Begomovirus (e.g., Cabbage leaf curl virus) encode an AL2 protein that is both a transcriptional activator and a silencing suppressor. The related L2 protein of Beet curly top virus (genus Curtovirus) lacks transcription activation activity. Previous studies showed that both AL2 and L2 suppress silencing by a mechanism that correlates with adenosine kinase (ADK) inhibition, while AL2 in addition activates transcription of cellular genes that negatively regulate silencing pathways. The goal of this study was to clarify the general means by which these viral proteins inhibit various aspects of silencing. We confirmed that AL2 inhibits systemic silencing spread by a mechanism that requires transcription activation activity. Surprisingly, we also found that reversal of PTGS and TGS by ADK inactivation depended on whether experiments were conducted in vegetative or reproductive Nicotiana benthamiana plants (i.e., before or after the vegetative-to-reproductive transition). While AL2 was able to reverse silencing in both vegetative and reproductive plants, L2 and ADK inhibition were effective only in vegetative plants. This suggests that silencing maintenance mechanisms can change during development or in response to stress. Remarkably, we also observed that AL2 lacking its transcription activation domain could reverse TGS in reproductive plants, revealing a third, previously unsuspected AL2 suppression mechanism that depends on neither ADK inactivation nor transcription activation. IMPORTANCE RNA silencing in plants is a multivalent antiviral defense, and viruses respond by elaborating multiple and sometimes multifunctional proteins that inhibit various aspects of silencing. The studies described here add an additional layer of complexity to this interplay. By examining geminivirus AL2 and L2 suppressor activities, we show that L2 is unable to suppress silencing in Nicotiana benthamiana plants that have undergone the vegetative-to-reproductive transition. As L2 was previously shown to be effective in mature Arabidopsis plants, these results illustrate that silencing mechanisms can change during development or in response to stress in ways that may be species specific. The AL2 and L2 proteins are known to share a suppression mechanism that correlates with the ability of both proteins to inhibit ADK, while AL2 in addition can inhibit silencing by transcriptionally activating cellular genes. Here, we also provide evidence for a third AL2 suppression mechanism that depends on neither transcription activation nor ADK inactivation. In addition to revealing the remarkable versatility of AL2, this work highlights the utility of viral suppressors as probes for the analysis of silencing pathways.
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Affiliation(s)
- Jamie N Jackel
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - R Cody Buchmann
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - Udit Singhal
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
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167
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Chilli leaf curl virus infection highlights the differential expression of genes involved in protein homeostasis and defense in resistant chilli plants. Appl Microbiol Biotechnol 2015; 99:4757-70. [DOI: 10.1007/s00253-015-6415-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/15/2015] [Accepted: 01/17/2015] [Indexed: 01/22/2023]
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168
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Paprotka T, Deuschle K, Pilartz M, Jeske H. Form follows function in geminiviral minichromosome architecture. Virus Res 2015; 196:44-55. [PMID: 25445344 DOI: 10.1016/j.virusres.2014.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
A comprehensive survey on the viral minichromosomes of the begomoviruses Abutilon mosaic virus, tomato yellow leaf curl Sardinia virus, African cassava mosaic virus, Indian cassava mosaic virus (family Geminiviridae) during the course of infections in Nicotiana benthamiana is summarized. Using optimized one-dimensional and two-dimensional gel systems combined with blot hybridization and a standardized evaluation, discrete and heterogeneous virus-specific signals with different DNA forms were compared to trace functions of viral multiplication with inactive/active replication and/or transcription. A quantitative approach to compare the distantly related viruses during the course of infection with the aim to generalize the conclusions for geminiviruses has been developed. Focussing on the distribution of topoisomers of viral supercoiled DNA, which reflect minichromosomal stages, predominant minichromosomes with 12 nucleosomes, less with 13 nucleosomes and no with 11 nucleosomes were found. These results indicate that chromatin with only one open gap to bind transcription factors is the favourite form. The dynamics during infections in dependence on the experimental conditions is discussed with reference to the design of experiments for resistance breeding and molecular analyses.
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Affiliation(s)
- Tobias Paprotka
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Kathrin Deuschle
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Marcel Pilartz
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Holger Jeske
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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169
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Niu D, Wang Z, Wang S, Qiao L, Zhao H. Profiling of small RNAs involved in plant-pathogen interactions. Methods Mol Biol 2015; 1287:61-79. [PMID: 25740356 DOI: 10.1007/978-1-4939-2453-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Small RNA (sRNA)-mediated gene silencing is an important gene expression regulatory mechanism conserved in eukaryotes. Such sRNAs, first discovered in plants, are involved in diverse biological processes. In plants, sRNAs participate in many growth and developmental processes, such as embryo development, seed germination, flowering, hormone synthesis and distribution, and nutrient assimilation. However, the significance of sRNA in shaping the relationship between plants and their symbiotic microbes or pathogens has been underestimated. Recent progress in profiling sRNA, especially advances in next-generation sequencing technology, has revealed its extensive and complicated involvement in interactions between plants and viruses, bacteria, and fungi. In this review, we will summarize recent findings regarding sRNA in plant-pathogen interactions.
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Affiliation(s)
- Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Xuanwu, Nanjing, Jiangsu, 210095, China
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170
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Sanchez DH, Paszkowski J. Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene. PLoS Genet 2014; 10:e1004806. [PMID: 25411840 PMCID: PMC4238952 DOI: 10.1371/journal.pgen.1004806] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/05/2014] [Indexed: 01/08/2023] Open
Abstract
Epigenetic mechanisms suppress the transcription of transposons and DNA repeats; however, this suppression can be transiently released under prolonged heat stress. Here we show that the Arabidopsis thaliana imprinted gene SDC, which is silent during vegetative growth due to DNA methylation, is activated by heat and contributes to recovery from stress. SDC activation seems to involve epigenetic mechanisms but not canonical heat-shock perception and signaling. The heat-mediated transcriptional induction of SDC occurs particularly in young developing leaves and is proportional to the level of stress. However, this occurs only above a certain window of absolute temperatures and, thus, resembles a thermal-sensing mechanism. In addition, the re-silencing kinetics during recovery can be entrained by repeated heat stress cycles, suggesting that epigenetic regulation in plants may conserve memory of stress experience. We further demonstrate that SDC contributes to the recovery of plant biomass after stress. We propose that transcriptional gene silencing, known to be involved in gene imprinting, is also co-opted in the specific tuning of SDC expression upon heat stress and subsequent recovery. It is therefore possible that dynamic properties of the epigenetic landscape associated with silenced or imprinted genes may contribute to regulation of their expression in response to environmental challenges. In plants, expression of certain imprinted genes is restricted to embryo nourishing tissue, the endosperm. Since these genes are silenced by epigenetic mechanisms during vegetative growth, it has been assumed that they have no role in this phase of the plant life cycle. Here, we report on heat-mediated release of epigenetic silencing and ectopic activation of the Arabidopsis thaliana endosperm-imprinted gene SDC. The stress induced activation of SDC involves epigenetic regulation but not the canonical heat-shock perception and signaling, and it seems to be required for efficient growth recovery after the stress. Our results exemplify a potential concealed role of an imprinted gene in plant responses to environmental challenges.
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Affiliation(s)
- Diego H. Sanchez
- University of Geneva, Laboratory of Plant Genetics-Sciences III, Genève, Switzerland
- * E-mail: (JP); (DHS)
| | - Jerzy Paszkowski
- University of Geneva, Laboratory of Plant Genetics-Sciences III, Genève, Switzerland
- * E-mail: (JP); (DHS)
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171
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Allie F, Pierce EJ, Okoniewski MJ, Rey C. Transcriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection. BMC Genomics 2014; 15:1006. [PMID: 25412561 PMCID: PMC4253015 DOI: 10.1186/1471-2164-15-1006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99] (SACMV). To date, there is limited gene regulation information on viral stress responses in cassava, and global transcriptome profiling in SACMV-infected cassava represents an important step towards understanding natural host responses to plant geminiviruses. RESULTS A RNA-seq time course (12, 32 and 67 dpi) study, monitoring gene expression in SACMV-challenged susceptible (T200) and tolerant (TME3) cassava landraces, was performed using the Applied Biosystems (ABI) SOLiD next-generation sequencing platform. The multiplexed paired end sequencing run produced a total of 523 MB and 693 MB of paired-end reads for SACMV-infected susceptible and tolerant cDNA libraries, respectively. Of these, approximately 50.7% of the T200 reads and 55.06% of TME3 reads mapped to the cassava reference genome available in phytozome. Using a log2 fold cut-off (p<0.05), comparative analysis between the six normalized cDNA libraries showed that 4181 and 1008 transcripts in total were differentially expressed in T200 and TME3, respectively, across 12, 32 and 67 days post infection, compared to mock-inoculated. The number of responsive transcripts increased dramatically from 12 to 32 dpi in both cultivars, but in contrast, in T200 the levels did not change significantly at 67 dpi, while in TME3 they declined. GOslim functional groups illustrated that differentially expressed genes in T200 and TME3 were overrepresented in the cellular component category for stress-related genes, plasma membrane and nucleus. Alterations in the expression of other interesting genes such as transcription factors, resistance (R) genes, and histone/DNA methylation-associated genes, were observed. KEGG pathway analysis uncovered important altered metabolic pathways, including phenylpropanoid biosynthesis, sucrose and starch metabolism, and plant hormone signalling. CONCLUSIONS Molecular mechanisms for TME3 tolerance are proposed, and differences in patterns and levels of transcriptome profiling between T200 and TME3 with susceptible and tolerant phenotypes, respectively, support the hypothesis that viruses rearrange their molecular interactions in adapting to hosts with different genetic backgrounds.
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Affiliation(s)
- Farhahna Allie
- />School of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein, Johannesburg, 2000 South Africa
| | - Erica J Pierce
- />School of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein, Johannesburg, 2000 South Africa
| | - Michal J Okoniewski
- />Functional Genomics Center, Zurich, UNI ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Chrissie Rey
- />School of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein, Johannesburg, 2000 South Africa
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172
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Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection. Proc Natl Acad Sci U S A 2014; 111:12942-7. [PMID: 25136118 DOI: 10.1073/pnas.1400894111] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV) and related begomoviruses are a major threat to tomato production worldwide and, to protect against these viruses, resistance genes from different wild tomato species are introgressed. Recently, the Ty-1 resistance gene was identified, shown to code for an RNA-dependent RNA polymerase and to be allelic with Ty-3. Here we show that upon TYLCV challenging of resistant lines carrying Ty-1 or Ty-3, low virus titers were detected concomitant with the production of relatively high levels of siRNAs whereas, in contrast, susceptible tomato Moneymaker (MM) revealed higher virus titers but lower amounts of siRNAs. Comparative analysis of the spatial genomic siRNA distribution showed a consistent and subtle enrichment for siRNAs derived from the V1 and C3 genes in Ty-1 and Ty-3. In plants containing Ty-2 resistance the virus was hardly detectable, but the siRNA profile resembled the one observed in TYLCV-challenged susceptible tomato (MM). Furthermore, a relative hypermethylation of the TYLCV V1 promoter region was observed in genomic DNA collected from Ty-1 compared with that from (MM). The resistance conferred by Ty-1 was also effective against the bipartite tomato severe rugose begomovirus, where a similar genome hypermethylation of the V1 promoter region was discerned. However, a mixed infection of TYLCV with cucumber mosaic virus compromised the resistance. The results indicate that Ty-1 confers resistance to geminiviruses by increasing cytosine methylation of viral genomes, suggestive of enhanced transcriptional gene silencing. The mechanism of resistance and its durability toward geminiviruses under natural field conditions is discussed.
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173
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Hefferon KL. DNA Virus Vectors for Vaccine Production in Plants: Spotlight on Geminiviruses. Vaccines (Basel) 2014; 2:642-53. [PMID: 26344750 PMCID: PMC4494219 DOI: 10.3390/vaccines2030642] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/16/2022] Open
Abstract
Plants represent a safe, efficacious and inexpensive production platform by which to provide vaccines and other therapeutic proteins to the world's poor. Plant virus expression vector technology has rapidly become one of the most popular methods to express pharmaceutical proteins in plants. This review discusses several of the state-of-the-art plant expression systems based upon geminiviruses that have been engineered for vaccine production. An overview of the advantages of these small, single-stranded DNA viruses is provided and comparisons are made with other virus expression systems. Advances in the design of several different geminivirus vectors are presented in this review, and examples of vaccines and other biologics generated from each are described.
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Affiliation(s)
- Kathleen L Hefferon
- Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 2J7, Canada.
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174
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Yong Chung H, Lacatus G, Sunter G. Geminivirus AL2 protein induces expression of, and interacts with, a calmodulin-like gene, an endogenous regulator of gene silencing. Virology 2014; 460-461:108-18. [PMID: 25010276 DOI: 10.1016/j.virol.2014.04.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/27/2014] [Accepted: 04/12/2014] [Indexed: 11/29/2022]
Abstract
RNA silencing is an innate cellular response involved in antiviral defense. Arabidopsis calmodulin-like protein 39 (At-rgsCaM) is related to known regulators of RNA silencing in tomato and Nicotiana tabacum. Geminivirus AL2 protein functions to suppress post-transcriptional and transcriptional gene silencing, possibly through induction of an endogenous regulator. In support of this, the At-rgsCaM promoter responds to Tomato golden mosaic virus (TGMV) AL2 in protoplasts and geminivirus infection increases rgsCaM expression in Arabidopsis and Nicotiana benthamiana. Further, over-expression of rgsCaM leads to increased susceptibility to infection, as a consequence of increased viral DNA loads. It has been shown that rgsCaM may target silencing suppressors of RNA viruses for degradation via the autophagy pathway. This interaction occurs within the cytoplasm, but AL2 interacts with rgsCaM in the nucleus. It is tempting to speculate that AL2 may act to sequester rgsCaM in the nucleus to prevent targeting of AL2 for degradation.
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Affiliation(s)
- Ho Yong Chung
- Department of Biology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Gabriela Lacatus
- Scripps Health/Hematology/Oncology Division, 15004 Innovation Dr., San Diego, CA 92128, USA
| | - Garry Sunter
- Department of Biology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA.
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175
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Bilichak A, Yao Y, Kovalchuk I. Transient down-regulation of the RNA silencing machinery increases efficiency of Agrobacterium-mediated transformation of Arabidopsis. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:590-600. [PMID: 24472037 DOI: 10.1111/pbi.12165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/15/2013] [Indexed: 06/03/2023]
Abstract
Agrobacterium tumefaciens is a plant pathogen that is widely used in plant transformation. As the process of transgenesis includes the delivery of single-stranded T-DNA molecule, we hypothesized that transformation rate may negatively correlate with the efficiency of the RNA-silencing machinery. Using mutants compromised in either the transcriptional or post-transcriptional gene-silencing pathways, two inhibitors of stable transformation were revealed-AGO2 and NRPD1a. Furthermore, an immunoprecipitation experiment has shown that NRPD1, a subunit of Pol IV, directly interacts with Agrobacterium T-DNA in planta. Using the Tobacco rattle virus (TRV)--based virus-induced gene silencing (VIGS) technique, we demonstrated that the transient down-regulation of the expression of either AGO2 or NRPD1a genes in reproductive organs of Arabidopsis, leads to an increase in transformation rate. We observed a 6.0- and 3.5-fold increase in transformation rate upon transient downregulation of either AGO2 or NRPD1a genes, respectively. This is the first report demonstrating the increase in the plant transformation rate via VIGS-mediated transient down-regulation of the components of epigenetic machinery in reproductive tissue.
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MESH Headings
- Agrobacterium/physiology
- Arabidopsis/genetics
- Arabidopsis/microbiology
- Arabidopsis Proteins/metabolism
- Blotting, Southern
- DNA Breaks, Double-Stranded
- DNA Methylation/genetics
- DNA, Bacterial/genetics
- DNA-Directed RNA Polymerases/metabolism
- Down-Regulation
- Epigenesis, Genetic
- Genes, Plant
- Genetic Loci
- Models, Genetic
- Mutation/genetics
- Plants, Genetically Modified
- Protein Binding
- Protein Subunits/metabolism
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Reverse Genetics
- Transformation, Genetic
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Affiliation(s)
- Andriy Bilichak
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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176
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Raja P, Jackel JN, Li S, Heard IM, Bisaro DM. Arabidopsis double-stranded RNA binding protein DRB3 participates in methylation-mediated defense against geminiviruses. J Virol 2014. [PMID: 24352449 DOI: 10.1128/jvi.02305-2313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
UNLABELLED Arabidopsis encodes five double-stranded RNA binding (DRB) proteins. DRB1 and DRB2 are involved in microRNA (miRNA) biogenesis, while DRB4 functions in cytoplasmic posttranscriptional small interfering RNA (siRNA) pathways. DRB3 and DRB5 are not involved in double-stranded RNA (dsRNA) processing but assist in silencing transcripts targeted by DRB2-associated miRNAs. The goal of this study was to determine which, if any, of the DRB proteins might also participate in a nuclear siRNA pathway that leads to geminivirus genome methylation. Here, we demonstrate that DRB3 functions with Dicer-like 3 (DCL3) and Argonaute 4 (AGO4) in methylation-mediated antiviral defense. Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses, using an RNA-directed DNA methylation (RdDM) pathway similar to that used to suppress endogenous invasive DNAs such as transposons. Chromatin methylation inhibits virus replication and transcription, and methylation-deficient host plants are hypersusceptible to geminivirus infection. Using a panel of drb mutants, we found that drb3 plants uniquely exhibit a similar hypersensitivity and that viral genome methylation is substantially reduced in drb3 compared to wild-type plants. In addition, like dcl3 and ago4 mutants, drb3 plants fail to recover from infection and cannot accomplish the viral genome hypermethylation that is invariably observed in asymptomatic, recovered tissues. Small RNA analysis, bimolecular fluorescence complementation, and coimmunoprecipitation experiments show that DRB3 acts downstream of siRNA biogenesis and suggest that it associates with DCL3 and AGO4 in distinct subnuclear compartments. These studies reveal that in addition to its previously established role in the miRNA pathway, DRB3 also functions in antiviral RdDM. IMPORTANCE Plants use RNA-directed DNA methylation (RdDM) as an epigenetic defense against geminiviruses. RNA silencing pathways in Arabidopsis include five double-stranded RNA binding proteins (DRBs) related to Drosophila R2D2 and mammalian TRBP and PACT. While DRB proteins have defined roles in miRNA and cytoplasmic siRNA pathways, a role in nuclear RdDM was elusive. Here, we used the geminivirus system to show that DRB3 is involved in methylation-mediated antiviral defense. Beginning with a panel of Arabidopsis drb mutants, we demonstrated that drb3 plants uniquely show enhanced susceptibility to geminiviruses. Further, like dcl3 and ago4 mutants, drb3 plants fail to hypermethylate the viral genome, a requirement for host recovery. We also show that DRB3 physically interacts with the RdDM pathway components DCL3 and AGO4 in the nucleus. This work highlights the utility of geminiviruses as models for de novo RdDM and places DRB3 protein in this fundamental epigenetic pathway.
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Affiliation(s)
- Priya Raja
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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177
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Miozzi L, Napoli C, Sardo L, Accotto GP. Transcriptomics of the interaction between the monopartite phloem-limited geminivirus tomato yellow leaf curl Sardinia virus and Solanum lycopersicum highlights a role for plant hormones, autophagy and plant immune system fine tuning during infection. PLoS One 2014; 9:e89951. [PMID: 24587146 PMCID: PMC3938563 DOI: 10.1371/journal.pone.0089951] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/25/2014] [Indexed: 12/13/2022] Open
Abstract
Tomato yellow leaf curl Sardinia virus (TYLCSV), a DNA virus belonging to the genus Begomovirus, causes severe losses in tomato crops. It infects only a limited number of cells in the vascular tissues, making difficult to detect changes in host gene expression linked to its presence. Here we present the first microarray study of transcriptional changes induced by the phloem-limited geminivirus TYLCSV infecting tomato, its natural host. The analysis was performed on the midrib of mature leaves, a material naturally enriched in vascular tissues. A total of 2206 genes were up-regulated and 1398 were down-regulated in infected plants, with an overrepresentation of genes involved in hormone metabolism and responses, nucleic acid metabolism, regulation of transcription, ubiquitin-proteasome pathway and autophagy among those up-regulated, and in primary and secondary metabolism, phosphorylation, transcription and methylation-dependent chromatin silencing among those down-regulated. Our analysis showed a series of responses, such as the induction of GA- and ABA-responsive genes, the activation of the autophagic process and the fine tuning of the plant immune system, observed only in TYLCSV-tomato compatible interaction so far. On the other hand, comparisons with transcriptional changes observed in other geminivirus-plant interactions highlighted common host responses consisting in the deregulation of biotic stress responsive genes, key enzymes in the ethylene biosynthesis and methylation cycle, components of the ubiquitin proteasome system and DNA polymerases II. The involvement of conserved miRNAs and of solanaceous- and tomato-specific miRNAs in geminivirus infection, investigated by integrating differential gene expression data with miRNA targeting data, is discussed.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
| | - Chiara Napoli
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
| | - Luca Sardo
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
- Viral Recombination Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Gian Paolo Accotto
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
- * E-mail:
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178
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Li F, Huang C, Li Z, Zhou X. Suppression of RNA silencing by a plant DNA virus satellite requires a host calmodulin-like protein to repress RDR6 expression. PLoS Pathog 2014; 10:e1003921. [PMID: 24516387 PMCID: PMC3916407 DOI: 10.1371/journal.ppat.1003921] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/24/2013] [Indexed: 11/19/2022] Open
Abstract
In plants, RNA silencing plays a key role in antiviral defense. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that target different effector molecules in the RNA silencing pathway. Evidence has shown that plants also encode endogenous suppressors of RNA silencing (ESRs) that function in proper regulation of RNA silencing. The possibility that these cellular proteins can be subverted by viruses to thwart host defense is intriguing but has not been fully explored. Here we report that the Nicotiana benthamiana calmodulin-like protein Nbrgs-CaM is required for the functions of the VSR βC1, the sole protein encoded by the DNA satellite associated with the geminivirus Tomato yellow leaf curl China virus (TYLCCNV). Nbrgs-CaM expression is up-regulated by the βC1. Transgenic plants over-expressing Nbrgs-CaM displayed developmental abnormities reminiscent of βC1-associated morphological alterations. Nbrgs-CaM suppressed RNA silencing in an Agrobacterium infiltration assay and, when over-expressed, blocked TYLCCNV-induced gene silencing. Genetic evidence showed that Nbrgs-CaM mediated the βC1 functions in silencing suppression and symptom modulation, and was required for efficient virus infection. Moreover, the tobacco and tomato orthologs of Nbrgs-CaM also possessed ESR activity, and were induced by betasatellite to promote virus infection in these Solanaceae hosts. We further demonstrated that βC1-induced Nbrgs-CaM suppressed the production of secondary siRNAs, likely through repressing RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) expression. RDR6-deficient N. benthamiana plants were defective in antiviral response and were hypersensitive to TYLCCNV infection. More significantly, TYLCCNV could overcome host range restrictions to infect Arabidopsis thaliana when the plants carried a RDR6 mutation. These findings demonstrate a distinct mechanism of VSR for suppressing PTGS through usurpation of a host ESR, and highlight an essential role for RDR6 in RNA silencing defense response against geminivirus infection.
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Affiliation(s)
- Fangfang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Changjun Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- 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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179
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Yang XL, Zhou MN, Qian YJ, Xie Y, Zhou XP. Molecular variability and evolution of a natural population of tomato yellow leaf curl virus in Shanghai, China. J Zhejiang Univ Sci B 2014; 15:133-42. [PMID: 24510706 PMCID: PMC3924389 DOI: 10.1631/jzus.b1300110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/21/2013] [Indexed: 11/11/2022]
Abstract
Tomato yellow leaf curl virus (TYLCV), belonging to the genus Begomovirus of the family Geminiviridae, is emerging as the most destructive pathogen of tomato plants. Since the first report of TYLCV in Shanghai, China in 2006, TYLCV has spread rapidly to 13 provinces or autonomous regions of China. In this study, the molecular variability and evolution of TYLCV were monitored in Shanghai from its first upsurge in 2006 until 2010. Full-length genomic sequences of 26 isolates were obtained by rolling circle amplification. Sequence analysis showed that the intergenic region was the most variable, with a mean mutation rate of 4.81×10(-3) nucleotide substitutions per site per year. Genetic differentiation was found within isolates obtained from 2006, 2009, and 2010, though a linear increase in genetic diversity over time was not evident. Whilst significant parts of TYLCV genes were under negative selection, the C4 gene embedded entirely within the C1 gene had a tendency to undergo positive selection. Our results indicate that a mechanism of independent evolution of overlapping regions could apply to the natural population of TYLCV in Shanghai, China.
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180
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Mohannath G, Jackel JN, Lee YH, Buchmann RC, Wang H, Patil V, Adams AK, Bisaro DM. A complex containing SNF1-related kinase (SnRK1) and adenosine kinase in Arabidopsis. PLoS One 2014; 9:e87592. [PMID: 24498147 PMCID: PMC3907550 DOI: 10.1371/journal.pone.0087592] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/30/2013] [Indexed: 12/22/2022] Open
Abstract
SNF1-related kinase (SnRK1) in plants belongs to a conserved family that includes sucrose non-fermenting 1 kinase (SNF1) in yeast and AMP-activated protein kinase (AMPK) in animals. These kinases play important roles in the regulation of cellular energy homeostasis and in response to stresses that deplete ATP, they inhibit energy consuming anabolic pathways and promote catabolism. Energy stress is sensed by increased AMP:ATP ratios and in plants, 5′-AMP inhibits inactivation of phosphorylated SnRK1 by phosphatase. In previous studies, we showed that geminivirus pathogenicity proteins interact with both SnRK1 and adenosine kinase (ADK), which phosphorylates adenosine to generate 5′-AMP. This suggested a relationship between SnRK1 and ADK, which we investigate in the studies described here. We demonstrate that SnRK1 and ADK physically associate in the cytoplasm, and that SnRK1 stimulates ADK in vitro by an unknown, non-enzymatic mechanism. Further, altering SnRK1 or ADK activity in transgenic plants altered the activity of the other kinase, providing evidence for in vivo linkage but also revealing that in vivo regulation of these activities is complex. This study establishes the existence of SnRK1-ADK complexes that may play important roles in energy homeostasis and cellular responses to biotic and abiotic stress.
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Affiliation(s)
- Gireesha Mohannath
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jamie N. Jackel
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Youn Hyung Lee
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, Korea
| | - R. Cody Buchmann
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Hui Wang
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Veena Patil
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Allie K. Adams
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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181
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Gomez A, Ingelman-Sundberg M. Pharmacoepigenetic aspects of gene polymorphism on drug therapies: effects of DNA methylation on drug response. Expert Rev Clin Pharmacol 2014; 2:55-65. [DOI: 10.1586/17512433.2.1.55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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182
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Wang B, Li F, Huang C, Yang X, Qian Y, Xie Y, Zhou X. V2 of tomato yellow leaf curl virus can suppress methylation-mediated transcriptional gene silencing in plants. J Gen Virol 2014; 95:225-230. [PMID: 24187017 DOI: 10.1099/vir.0.055798-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV) is a DNA virus belonging to the genus Begomovirus. TYLCV replicates using double-stranded DNA intermediates that can become the target of plant transcriptional gene silencing (TGS). Here, we show that the V2 protein of TYLCV can suppress TGS of a transcriptionally silenced green fluorescent protein (GFP) transgene in Nicotiana benthamiana line 16-TGS. Through bisulfite sequencing and chop-PCR, we demonstrated that the TYLCV V2 can reverse GFP transgene silencing by reducing the methylation levels in the 35S promoter sequence. Both AtSN1 and MEA-ISR loci in Arabidopsis thaliana were previously reported to be strongly methylated, and we show that the methylation status of both loci was significantly reduced in TYLCV V2 transgenic Arabidopsis plants. We conclude that TYLCV can efficiently suppress TGS when it infects plants, and its V2 protein is responsible for the TGS suppression activity.
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Affiliation(s)
- Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Fangfang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Changjun Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Xiuling Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Yajuan Qian
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
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183
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Arabidopsis double-stranded RNA binding protein DRB3 participates in methylation-mediated defense against geminiviruses. J Virol 2013; 88:2611-22. [PMID: 24352449 DOI: 10.1128/jvi.02305-13] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Arabidopsis encodes five double-stranded RNA binding (DRB) proteins. DRB1 and DRB2 are involved in microRNA (miRNA) biogenesis, while DRB4 functions in cytoplasmic posttranscriptional small interfering RNA (siRNA) pathways. DRB3 and DRB5 are not involved in double-stranded RNA (dsRNA) processing but assist in silencing transcripts targeted by DRB2-associated miRNAs. The goal of this study was to determine which, if any, of the DRB proteins might also participate in a nuclear siRNA pathway that leads to geminivirus genome methylation. Here, we demonstrate that DRB3 functions with Dicer-like 3 (DCL3) and Argonaute 4 (AGO4) in methylation-mediated antiviral defense. Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses, using an RNA-directed DNA methylation (RdDM) pathway similar to that used to suppress endogenous invasive DNAs such as transposons. Chromatin methylation inhibits virus replication and transcription, and methylation-deficient host plants are hypersusceptible to geminivirus infection. Using a panel of drb mutants, we found that drb3 plants uniquely exhibit a similar hypersensitivity and that viral genome methylation is substantially reduced in drb3 compared to wild-type plants. In addition, like dcl3 and ago4 mutants, drb3 plants fail to recover from infection and cannot accomplish the viral genome hypermethylation that is invariably observed in asymptomatic, recovered tissues. Small RNA analysis, bimolecular fluorescence complementation, and coimmunoprecipitation experiments show that DRB3 acts downstream of siRNA biogenesis and suggest that it associates with DCL3 and AGO4 in distinct subnuclear compartments. These studies reveal that in addition to its previously established role in the miRNA pathway, DRB3 also functions in antiviral RdDM. IMPORTANCE Plants use RNA-directed DNA methylation (RdDM) as an epigenetic defense against geminiviruses. RNA silencing pathways in Arabidopsis include five double-stranded RNA binding proteins (DRBs) related to Drosophila R2D2 and mammalian TRBP and PACT. While DRB proteins have defined roles in miRNA and cytoplasmic siRNA pathways, a role in nuclear RdDM was elusive. Here, we used the geminivirus system to show that DRB3 is involved in methylation-mediated antiviral defense. Beginning with a panel of Arabidopsis drb mutants, we demonstrated that drb3 plants uniquely show enhanced susceptibility to geminiviruses. Further, like dcl3 and ago4 mutants, drb3 plants fail to hypermethylate the viral genome, a requirement for host recovery. We also show that DRB3 physically interacts with the RdDM pathway components DCL3 and AGO4 in the nucleus. This work highlights the utility of geminiviruses as models for de novo RdDM and places DRB3 protein in this fundamental epigenetic pathway.
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184
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Pumplin N, Voinnet O. RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 2013; 11:745-60. [PMID: 24129510 DOI: 10.1038/nrmicro3120] [Citation(s) in RCA: 391] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA silencing is a central regulator of gene expression in most eukaryotes and acts both at the transcriptional level through DNA methylation and at the post-transcriptional level through direct mRNA interference mediated by small RNAs. In plants and invertebrates, the same pathways also function directly in host defence against viruses by targeting viral RNA for degradation. Successful viruses have consequently evolved diverse mechanisms to avoid silencing, most notably through the expression of viral suppressors of RNA silencing. RNA silencing suppressors have also been recently identified in plant pathogenic bacteria and oomycetes, suggesting that disruption of host silencing is a general virulence strategy across several kingdoms of plant pathogens. There is also increasing evidence that plants have evolved specific defences against RNA-silencing suppression by pathogens, providing yet another illustration of the never-ending molecular arms race between plant pathogens and their hosts.
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Affiliation(s)
- Nathan Pumplin
- Swiss Federal Institute of Technology Zurich (ETH-Zurich), Department of Biology, Zurich, Switzerland
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185
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Medina-Hernández D, Rivera-Bustamante RF, Tenllado F, Holguín-Peña RJ. Effects and effectiveness of two RNAi constructs for resistance to Pepper golden mosaic virus in Nicotiana benthamiana plants. Viruses 2013; 5:2931-45. [PMID: 24287597 PMCID: PMC3967154 DOI: 10.3390/v5122931] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/14/2013] [Accepted: 11/20/2013] [Indexed: 01/11/2023] Open
Abstract
ToChLPV and PepGMV are Begomoviruses that have adapted to a wide host range and are able to cause major diseases in agronomic crops. We analyzed the efficacy of induced resistance to PepGMV in Nicotiana benthamiana plants with two constructs: one construct with homologous sequences derived from PepGMV, and the other construct with heterologous sequences derived from ToChLPV. Plants protected with the heterologous construct showed an efficacy to decrease the severity of symptoms of 45%, while plants protected with the homologous construct showed an efficacy of 80%. Plants protected with the heterologous construct showed a reduction of incidence of 42.86%, while the reduction of incidence in plants protected with the homologous construct was 57.15%. The efficacy to decrease viral load was 95.6% in plants protected with the heterologous construct, and 99.56% in plants protected with the homologous construct. We found, in both constructs, up-regulated key components of the RNAi pathway. This demonstrates that the efficacy of the constructs was due to the activation of the gene silencing mechanism, and is reflected in the decrease of viral genome copies, as well as in recovery phenotype. We present evidence that both constructs are functional and can efficiently induce transient resistance against PepGMV infections. This observation guarantees a further exploration as a strategy to control complex Begomovirus diseases in the field.
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Affiliation(s)
- Diana Medina-Hernández
- Laboratorio de Fitopatología, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur, 23096, Mexico; E-Mails: (R.J.H.P.); (D.M.H.)
| | - Rafael Francisco Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Km. 9.6 Libramiento Norte, Irapuato, Guanajuato, 36821, Mexico; E-Mail: (R.F.R.B.)
| | - Francisco Tenllado
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, Madrid, 28040, Spain; E-Mail: (F.T.)
| | - Ramón Jaime Holguín-Peña
- Laboratorio de Fitopatología, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur, 23096, Mexico; E-Mails: (R.J.H.P.); (D.M.H.)
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186
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Hanley-Bowdoin L, Bejarano ER, Robertson D, Mansoor S. Geminiviruses: masters at redirecting and reprogramming plant processes. Nat Rev Microbiol 2013; 11:777-88. [DOI: 10.1038/nrmicro3117] [Citation(s) in RCA: 484] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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187
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Miozzi L, Pantaleo V, Burgyán J, Accotto GP, Noris E. Analysis of small RNAs derived from tomato yellow leaf curl Sardinia virus reveals a cross reaction between the major viral hotspot and the plant host genome. Virus Res 2013; 178:287-96. [PMID: 24091361 DOI: 10.1016/j.virusres.2013.09.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
RNA silencing is a defense mechanism exploited by plants against viruses. Upon infection, viral genomes and their transcripts are processed by Dicer-like (DCL) ribonucleases into viral small interfering RNAs (vsRNAs) of 21-24 nucleotides that further guide silencing of viral transcripts. To get an insight into the molecular interaction between tomato and the monopartite phloem-limited begomovirus tomato yellow leaf curl Sardinia virus (TYLCSV), a pathogen inducing a devastating disease of tomato in the Mediterranean region, we characterized by deep sequencing the vsRNA population in virus-infected tomato plants, using a Solexa/Illumina platform. TYLCSV-sRNAs spanned the entire viral genome but were discontinuously distributed throughout it, with a prevalence from the transcribed regions. TYLCSV-sRNAs were mainly 21-22 nucleotides in length and their polarity was asymmetrically distributed along the genome. The most abundant vsRNAs originated from a narrow region overlapping the Rep/C4 genes and from a broader region including the end of the V2 and the beginning of the coat protein genes. Deep sequencing results were validated by different hybridization techniques. Comparisons with the data available on vsRNAs for other begomoviruses highlighted both similarities and differences. Host-derived RNA species cross-reacting with a portion of the viral genome corresponding to the most abundant vsRNAs hotspot were detected. Bioinformatics analyses were carried out to investigate the nature of these host molecules.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 101035 Torino, Italy
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188
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Peláez P, Sanchez F. Small RNAs in plant defense responses during viral and bacterial interactions: similarities and differences. FRONTIERS IN PLANT SCIENCE 2013; 4:343. [PMID: 24046772 PMCID: PMC3763480 DOI: 10.3389/fpls.2013.00343] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 05/20/2023]
Abstract
Small non-coding RNAs constitute an important class of gene expression regulators that control different biological processes in most eukaryotes. In plants, several small RNA (sRNA) silencing pathways have evolved to produce a wide range of small RNAs with specialized functions. Evidence for the diverse mode of action of the small RNA pathways has been highlighted during plant-microbe interactions. Host sRNAs and small RNA silencing pathways have been recognized as essential components of plant immunity. One way plants respond and defend against pathogen infections is through the small RNA silencing immune system. To deal with plant defense responses, pathogens have evolved sophisticated mechanisms to avoid and counterattack this defense strategy. The relevance of the small RNA-mediated plant defense responses during viral infections has been well-established. Recent evidence points out its importance also during plant-bacteria interactions. Herein, this review discusses recent findings, similarities and differences about the small RNA-mediated arms race between plants and these two groups of microbes, including the small RNA silencing pathway components that contribute to plant immune responses, the pathogen-responsive endogenous sRNAs and the pathogen-delivered effector proteins.
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Affiliation(s)
| | - Federico Sanchez
- *Correspondence: Federico Sanchez, Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, 62210 Cuernavaca, Morelos, México e-mail:
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189
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Cañizares MC, Lozano-Durán R, Canto T, Bejarano ER, Bisaro DM, Navas-Castillo J, Moriones E. Effects of the crinivirus coat protein-interacting plant protein SAHH on post-transcriptional RNA silencing and its suppression. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1004-15. [PMID: 23697374 DOI: 10.1094/mpmi-02-13-0037-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In plants, post-transcriptional gene silencing (PTGS) is a sequence-specific mechanism of RNA degradation induced by double-stranded RNA (dsRNA), which is processed into small interfering RNAs (siRNAs). siRNAs are methylated and, thereby, stabilized by the activity of the S-adenosylmethionine-dependent RNA methyltransferase HEN1. PTGS is amplified by host-encoded RNA-dependent RNA polymerases (RDR), which generate dsRNA that is processed into secondary siRNAs. To counteract this RNA silencing-mediated response of the host, plant viruses express proteins with silencing suppression activity. Here, we report that the coat protein (CP) of crinivirus (family Closteroviridae, genus Crinivirus) Tomato chlorosis virus, a known suppressor of silencing, interacts with S-adenosylhomocysteine hydrolase (SAHH), a plant protein essential for sustaining the methyl cycle and S-adenosylmethionine-dependent methyltransferase activity. Our results show that, by contributing to an increased accumulation of secondary siRNAs generated by the action of RDR6, SAHH enhances local RNA silencing. Although downregulation of SAHH prevents local silencing, it enhances the spread of systemic silencing. Our results also show that SAHH is important in the suppression of local RNA silencing not only by the crinivirus Tomato chlorosis virus CP but also by the multifunctional helper component-proteinase of the potyvirus Potato virus Y.
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Affiliation(s)
- M Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas IHSM-UMA-CSIC, Estación Experimental La Mayora, Málaga, Spain
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190
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Xie Y, Zhao L, Jiao X, Jiang T, Gong H, Wang B, Briddon RW, Zhou X. A recombinant begomovirus resulting from exchange of the C4 gene. J Gen Virol 2013; 94:1896-1907. [PMID: 23720217 DOI: 10.1099/vir.0.053181-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A begomovirus isolated from Malvastrum coromandelianum and tomato originating from Yunnan province (China) was shown to be representative of a new begomovirus species, for which the name tomato leaf curl Yunnan virus (TLCYnV) is proposed. TLCYnV has high levels of sequence identity to tomato yellow leaf curl China virus (TYLCCNV) across the whole genome, except for sequences encompassing the C4 gene. Agrobacterium-mediated inoculation showed TLCYnV to be highly infectious to a range of plant species but poorly infectious to M. coromandelianum. In contrast to TYLCCNV, TLCYnV was shown to infect tomato in the absence of a betasatellite. In field-collected samples, TLCYnV was identified most frequently in tomato in which it was not associated with a betasatellite. Transgenic expression in Nicotiana benthamiana showed that the C4 protein of TYLCCNV did not induce developmental abnormalities, whereas the C4 of TLCYnV induced severe developmental abnormalities, reminiscent of virus symptoms. The genome of TLCYnV was shown to be significantly less methylated in plants than that of TYLCCNV and the C4 protein of TLCYnV was shown to suppress post-transcriptional gene silencing and transcriptional gene silencing more effectively than the C4 of TYLCCNV. The results indicate that TLCYnV evolved from TYLCCNV by recombination, acquiring a more virulent C4, allowing it to dispense with the requirement for a betasatellite. The implications of these findings in relation to the evolution of monopartite begomoviruses are discussed.
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Affiliation(s)
- Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Liling Zhao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaoyang Jiao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Tong Jiang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Huanran Gong
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, P.O. Box 577, Faisalabad, Pakistan
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
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191
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Pooggin MM. How can plant DNA viruses evade siRNA-directed DNA methylation and silencing? Int J Mol Sci 2013; 14:15233-59. [PMID: 23887650 PMCID: PMC3759858 DOI: 10.3390/ijms140815233] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/01/2013] [Accepted: 07/01/2013] [Indexed: 11/16/2022] Open
Abstract
Plants infected with DNA viruses produce massive quantities of virus-derived, 24-nucleotide short interfering RNAs (siRNAs), which can potentially direct viral DNA methylation and transcriptional silencing. However, growing evidence indicates that the circular double-stranded DNA accumulating in the nucleus for Pol II-mediated transcription of viral genes is not methylated. Hence, DNA viruses most likely evade or suppress RNA-directed DNA methylation. This review describes the specialized mechanisms of replication and silencing evasion evolved by geminiviruses and pararetoviruses, which rescue viral DNA from repressive methylation and interfere with transcriptional and post-transcriptional silencing of viral genes.
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Affiliation(s)
- Mikhail M Pooggin
- University of Basel, Department of Environmental Sciences, Botany, Schönbeinstrasse 6, Basel 4056, Switzerland.
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192
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Incarbone M, Dunoyer P. RNA silencing and its suppression: novel insights from in planta analyses. TRENDS IN PLANT SCIENCE 2013; 18:382-92. [PMID: 23684690 DOI: 10.1016/j.tplants.2013.04.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/25/2013] [Accepted: 04/04/2013] [Indexed: 05/19/2023]
Abstract
Plants employ multiple layers of innate immunity to fight pathogens. For both RNA and DNA viruses, RNA silencing plays a critical role in plant resistance. To escape this antiviral silencing-based immune response, viruses have evolved various counterdefense strategies, the most widespread being production of viral suppressors of RNA silencing (VSRs) that target various stages of the silencing mechanisms. Recent findings from in planta analyses have provided new insights into the mode of action of VSRs and revealed that plants react to the perturbation of the silencing pathways brought by viral infection by deploying a battery of counter-counterdefense measures. As well as discussing which experimental approaches have been most effective in delivering clear and unambiguous results, this review provides a detailed account of the surprising variety of offensive and defensive strategies set forth by both viruses and hosts in their struggle for survival.
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Affiliation(s)
- Marco Incarbone
- IBMP-CNRS, 12 rue du General Zimmer, 67084 Strasbourg Cedex, France
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193
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Joel AJ. Epigenetic responses to drought stress in rice (Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:379-87. [PMID: 24431506 PMCID: PMC3715639 DOI: 10.1007/s12298-013-0176-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Cytosine methylation polymorphism plays a key role in gene regulation, mainly in expression of genes in crop plants. The differential expression of cytosine methylation over drought stress response was analyzed in rice using drought susceptible but agronomically superior lines IR 20 and CO 43, and drought tolerant genotypes PL and PMK 3 and their F1 hybrids. The parents and hybrids were subjected to two moisture regimes viz., one under drought condition and another under control condition. The cytosine methylation polymorphism in genomic DNA was quantified under both the conditions at the reproductive stage of the plant using the Methylation Sensitive Amplified Polymorphism (MSAP) technique devised by Xiong et al. (261:439-446, 1999). The results depicted that under drought condition, hyper-methylation was predominant in the drought susceptible genotypes while drought tolerant genotypes presented hypo-methylation behavior. While imposing drought, spikelet sterility per cent was positively correlated to percentage of methylation whereas, panicle length, number of seed per panicle, panicle weight, 100 seed weight, and yield/plant were negatively correlated indicating the role of epigenetic regulation in yield attributing traits in response to drought. Thus, methylation can be considered as an important epigenetic regulatory mechanism in rice plants to adapt drought situation. From this study, we speculate that the hyper- methylation may be an indicator of drought susceptibility and the hypo-methylation for drought tolerance and this methylation polymorphism can be effectively used in drought screening program.
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Affiliation(s)
- A. John Joel
- />Department of Plant Genetic Resources, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003 India
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194
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Rodríguez-Negrete E, Lozano-Durán R, Piedra-Aguilera A, Cruzado L, Bejarano ER, Castillo AG. Geminivirus Rep protein interferes with the plant DNA methylation machinery and suppresses transcriptional gene silencing. THE NEW PHYTOLOGIST 2013; 199:464-475. [PMID: 23614786 DOI: 10.1111/nph.12286] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/13/2013] [Indexed: 05/17/2023]
Abstract
Cytosine methylation is an epigenetic mark that promotes gene silencing and plays an important role in genome defence against transposons and invading DNA viruses. Previous data showed that the largest family of single-stranded DNA viruses, Geminiviridae, prevents methylation-mediated transcriptional gene silencing (TGS) by interfering with the proper functioning of the plant methylation cycle. Here, we describe a novel counter-defence strategy used by geminiviruses, which reduces the expression of the plant maintenance DNA methyltransferases, METHYLTRANSFERASE 1 (MET1) and CHROMOMETHYLASE 3 (CMT3), in both locally and systemically infected tissues. We demonstrated that the virus-mediated repression of these two maintenance DNA methyltransferases is widespread among geminivirus species. Additionally, we identified Rep (Replication associated protein) as the geminiviral protein responsible for the repression of MET1 and CMT3, and another viral protein, C4, as an ancillary player in MET1 down-regulation. The presence of Rep suppressed TGS of an Arabidopsis thaliana transgene and of host loci whose expression was strongly controlled by CG methylation. Bisulfite sequencing analyses showed that the expression of Rep caused a substantial reduction in the levels of DNA methylation at CG sites. Our findings suggest that Rep, the only viral protein essential for replication, displays TGS suppressor activity through a mechanism distinct from that thus far described for geminiviruses.
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Affiliation(s)
- Edgar Rodríguez-Negrete
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Rosa Lozano-Durán
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Alvaro Piedra-Aguilera
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Lucia Cruzado
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Eduardo R Bejarano
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Araceli G Castillo
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
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195
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Carmo LST, Resende RO, Silva LP, Ribeiro SG, Mehta A. Identification of host proteins modulated by the virulence factor AC2 of Tomato chlorotic mottle virus in Nicotiana benthamiana. Proteomics 2013; 13:1947-60. [PMID: 23533094 DOI: 10.1002/pmic.201200547] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/08/2013] [Accepted: 02/25/2013] [Indexed: 11/09/2022]
Abstract
Tomato, one of the most important crops cultivated worldwide, has been severely affected by begomoviruses such as the Tomato chlorotic mottle virus (ToCMoV). Virulence factor AC2 is considered crucial for a successful virus-plant interaction and is known to act as a transcriptional activator and in some begomoviruses to function as an RNA silencing suppressor factor. However, the exact functions of the AC2 protein of the begomovirus ToCMoV are not yet established. The aim of the present study was to identify differentially expressed proteins of the model plant Nicotiana benthamiana in response to the expression of the AC2 gene, isolated from ToCMoV. N. benthamiana plants were inoculated with Agrobacterium tumefaciens containing the viral vector Potato virus X (PVX) and with the PVX-AC2 construction. 2DE was performed and proteins were identified by MS. The results showed that the expression of ToCMoV AC2 alters the levels of several host proteins, which are important for normal plant development, causing an imbalance in cellular homeostasis. This study highlights the effect of AC2 in the modulation of plant defense processes by increasing the expression of several oxidative stress-related and pathogenesis-related proteins, as well as its role in modulating the proteome of the photosynthesis and energy production systems.
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196
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Seo JK, Wu J, Lii Y, Li Y, Jin H. Contribution of small RNA pathway components in plant immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:617-25. [PMID: 23489060 PMCID: PMC3752434 DOI: 10.1094/mpmi-10-12-0255-ia] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Small RNAs regulate a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity, in a sequence-specific manner. Accumulating evidence reveals that host endogenous small RNAs and small RNA pathway components play important roles in plant immune responses against various pathogens, including bacteria, fungi, oomycetes, and viruses. Small-RNA-mediated defense responses are regulated through diverse pathways and the components of these pathways, including Dicer-like proteins, RNA-dependent RNA polymerases, Argonaute proteins, and RNA polymerase IV and V, exhibit functional specificities as well as redundancy. In this review, we summarize the recent insights revealed mainly through the examination of two model plants, Arabidopsis and rice, with a primary focus on our emerging understanding of how these small RNA pathway components contribute to plant immunity.
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Affiliation(s)
- Jang-Kyun Seo
- Department of Plant Pathology & Microbiology, University of California, Riverside, CA, USA
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197
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Sabin LR, Cherry S. Small creatures use small RNAs to direct antiviral defenses. Eur J Immunol 2013; 43:27-33. [PMID: 23322691 DOI: 10.1002/eji.201243201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 11/27/2012] [Accepted: 12/12/2012] [Indexed: 11/09/2022]
Abstract
Antiviral RNA silencing has been recognized as an important defense mechanism in arthropods against RNA viruses. However, the role of this pathway in DNA virus infection remains largely unexplored. A report in this issue of the European Journal of Immunology provides new insight into the role of RNA silencing in antiviral defense against DNA viruses. Huang and Zhang [Eur. J. Immunol. 2013. 137-146] found that the dsDNA virus white spot syndrome virus, an agriculturally important pathogen of shrimp, is targeted by the shrimp RNA-silencing machinery via the production of virus-derived siRNAs. Furthermore, the authors show that the RNA-silencing pathway, and crucially, Dicer-2, is important for restricting viral infection. This study provides novel insights not only into shrimp antiviral defenses but also potentially into antiviral immunity against DNA viruses in a larger spectrum of hosts, as discussed in this Commentary. Furthermore, this study may contribute to the future development of immune-based therapeutics to combat viral pathogens, not only in aquaculture, but also in insect vectors of human diseases.
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Affiliation(s)
- Leah R Sabin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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198
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Yang LP, Fang YY, An CP, Dong L, Zhang ZH, Chen H, Xie Q, Guo HS. C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with beet severe curly top virus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:910-7. [PMID: 23176533 DOI: 10.1111/tpj.12081] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 05/20/2023]
Abstract
Cytosine methylation is one of epigenetic information marked on the DNA sequence. In plants, small interfering RNAs (siRNAs) target homologous genomic DNA sequences for cytosine methylation. This process, known as RNA-directed DNA methylation (RdDM), plays an important role in transposon control, regulation of gene expression and virus resistance. In this paper, we demonstrate that the C2 protein encoded by a geminivirus (beet severe curly top virus, BSCTV) mediated a decrease in DNA methylation of repeat regions in the promoters of ACD6, an upstream regulator of the salicylic acid defense pathway, and GSTF14, an endogenous gene of the glutathione S-transferase superfamily that is implicated in numerous stress responses. C2-mediated decreases in DNA methylation reduced accumulation of the siRNAs derived from the promoter repeats and enhanced the steady-state expression of both ACD6 and GSTF14 transcripts. Reduced accumulation of BSCTV-derived siRNAs was detected in BSCTV-infected plants, but not in plants infected with C2-deficient BSCTV (c2(- ) BSCTV). C2 protein exhibited no siRNA-binding activity. Instead, our results revealed that C2 protein-mediated decreases in DNA methylation appeared to affect the production of siRNAs that are required for targeting and reinforcing RdDM, a process that activated expression of defense-related genes that are normally dampened by these siRNAs in the host plants. However, C2-dependent reduction in virus-derived siRNAs also benefits the viruses by disrupting the feedback loop reinforcing DNA methylation-mediated antiviral silencing.
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Affiliation(s)
- Li-Ping Yang
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Beijing, 100101, China
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199
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Verlaan MG, Hutton SF, Ibrahem RM, Kormelink R, Visser RGF, Scott JW, Edwards JD, Bai Y. The Tomato Yellow Leaf Curl Virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA-dependent RNA polymerases. PLoS Genet 2013; 9:e1003399. [PMID: 23555305 PMCID: PMC3610679 DOI: 10.1371/journal.pgen.1003399] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/04/2013] [Indexed: 12/11/2022] Open
Abstract
Tomato Yellow Leaf Curl Virus Disease incited by Tomato yellow leaf curl virus (TYLCV) causes huge losses in tomato production worldwide and is caused by different related begomovirus species. Breeding for TYLCV resistance has been based on the introgression of multiple resistance genes originating from several wild tomato species. In this study we have fine-mapped the widely used Solanum chilense-derived Ty-1 and Ty-3 genes by screening nearly 12,000 plants for recombination events and generating recombinant inbred lines. Multiple molecular markers were developed and used in combination with disease tests to fine-map the genes to a small genomic region (approximately 70 kb). Using a Tobacco Rattle Virus-Virus Induced Gene Silencing approach, the resistance gene was identified. It is shown that Ty-1 and Ty-3 are allelic and that they code for a RNA-dependent RNA polymerase (RDR) belonging to the RDRγ type, which has an atypical DFDGD motif in the catalytic domain. In contrast to the RDRα type, characterized by a catalytic DLDGD motif, no clear function has yet been described for the RDRγ type, and thus the Ty-1/Ty-3 gene unveils a completely new class of resistance gene. Although speculative, the resistance mechanism of Ty-1/Ty-3 and its specificity towards TYLCV are discussed in light of the function of the related RDRα class in the amplification of the RNAi response in plants and transcriptional silencing of geminiviruses in plants.
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Affiliation(s)
- Maarten G. Verlaan
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Samuel F. Hutton
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, United States of America
| | - Ragy M. Ibrahem
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, United States of America
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Richard G. F. Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - John W. Scott
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, United States of America
| | - Jeremy D. Edwards
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, United States of America
| | - Yuling Bai
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
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200
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Both OsRecQ1 and OsRDR1 are required for the production of small RNA in response to DNA-damage in rice. PLoS One 2013; 8:e55252. [PMID: 23383126 PMCID: PMC3559376 DOI: 10.1371/journal.pone.0055252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 12/27/2012] [Indexed: 12/04/2022] Open
Abstract
Small RNA-mediated gene silencing pathways play important roles in the regulation of development, genome stability and various stress responses in many eukaryotes. Recently, a new type of small interfering RNAs (qiRNAs) approximately 20–21 nucleotides long in Neurospora crassa have been shown to mediate gene silencing in the DNA damage response (DDR) pathway. However, the mechanism for RNA silencing in the DDR pathway is largely unknown in plants. Here, we report that a class of small RNAs (qiRNAs) derived from rDNA was markedly induced after treatment by DNA-damaging agents [ethyl methanesulphonate (EMS and UV-C)], and that aberrant RNAs (aRNAs) as precursors were also highly induced after the DNA damage treatment in rice. However, these RNAs were completely abolished in OsRecQ1 (RecQ DNA helicase homologue) and OsRDR1 (RNA-dependent RNA polymerase homologue) mutant lines where either gene was disrupted by the insertion of rice retrotransposon Tos17 after the same treatment. DNA damage resulted in a more significant increase in cell death and a more severe inhibition of root growth in both mutant lines than in the WT. Together, these results strongly suggest that both OsRecQ1 and OsRDR1 play a pivotal role in the aRNA and qiRNA biogenesis required for the DDR and repair pathway in rice, and it may be a novel mechanism of regulation to the DDR through the production of qiRNA in plants.
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