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Ying X, Bera S, Liu J, Toscano-Morales R, Jang C, Yang S, Ho J, Simon AE. Umbravirus-like RNA viruses are capable of independent systemic plant infection in the absence of encoded movement proteins. PLoS Biol 2024; 22:e3002600. [PMID: 38662792 PMCID: PMC11081511 DOI: 10.1371/journal.pbio.3002600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 05/09/2024] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
The signature feature of all plant viruses is the encoding of movement proteins (MPs) that supports the movement of the viral genome into adjacent cells and through the vascular system. The recent discovery of umbravirus-like viruses (ULVs), some of which only encode replication-associated proteins, suggested that they, as with umbraviruses that lack encoded capsid proteins (CPs) and silencing suppressors, would require association with a helper virus to complete an infection cycle. We examined the infection properties of 2 ULVs: citrus yellow vein associated virus 1 (CY1), which only encodes replication proteins, and closely related CY2 from hemp, which encodes an additional protein (ORF5CY2) that was assumed to be an MP. We report that both CY1 and CY2 can independently infect the model plant Nicotiana benthamiana in a phloem-limited fashion when delivered by agroinfiltration. Unlike encoded MPs, ORF5CY2 was dispensable for infection of CY2, but was associated with faster symptom development. Examination of ORF5CY2 revealed features more similar to luteoviruses/poleroviruses/sobemovirus CPs than to 30K class MPs, which all share a similar single jelly-roll domain. In addition, only CY2-infected plants contained virus-like particles (VLPs) associated with CY2 RNA and ORF5CY2. CY1 RNA and a defective (D)-RNA that arises during infection interacted with host protein phloem protein 2 (PP2) in vitro and in vivo, and formed a high molecular weight complex with sap proteins in vitro that was partially resistant to RNase treatment. When CY1 was used as a virus-induced gene silencing (VIGS) vector to target PP2 transcripts, CY1 accumulation was reduced in systemic leaves, supporting the usage of PP2 for systemic movement. ULVs are therefore the first plant viruses encoding replication and CPs but no MPs, and whose systemic movement relies on a host MP. This explains the lack of discernable helper viruses in many ULV-infected plants and evokes comparisons with the initial viruses transferred into plants that must have similarly required host proteins for movement.
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Affiliation(s)
- Xiaobao Ying
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jinyuan Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Roberto Toscano-Morales
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Chanyong Jang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Stephen Yang
- Silvec Biologics, Inc., Gaithersburg, Maryland, United States of America
| | - Jovia Ho
- Silvec Biologics, Inc., Gaithersburg, Maryland, United States of America
| | - Anne E. Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- Silvec Biologics, Inc., Gaithersburg, Maryland, United States of America
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2
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Ghorbani A, Faghihi MM, Falaki F, Izadpanah K. Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. PLoS One 2023; 18:e0288068. [PMID: 37384654 PMCID: PMC10310044 DOI: 10.1371/journal.pone.0288068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023] Open
Abstract
Citrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into several genotypes. In recent years, some orange citrumelo-tolerant rootstocks showed yellowing, decline, and vein clearing in northern Iran (Mazandaran province, Sari). We confirmed the presence of CTV in the symptomatic trees by reverse transcription PCR (RT-PCR). The complete genome of a Sari isolate of CTV (Sari isolate) was sequenced using next-generation sequencing (NGS) technology. In addition, phylogenetic analysis, differential gene expression of the virus and identification of its variants in a population were studied. We obtained the final contigs of the virus (nt) and annotated all genomes to viral ORFs, untranslated regions (UTRs), intergenic regions, and 5' and 3' ends of the genome. Phylogenetic analysis of the Sari isolate and other genotypes of CTV showed that the Sari isolates were placed in a distinct cluster without a sister group. Based on the number of specific transcripts (TPM) in CTV RNA -Seq, P13 was the most highly expressed gene related to the host range of the virus and its systemic infection. The ORFs of the polyprotein, P33, and P18 showed variation in a single population of the sari isolate. The CTV has a potential for variation in a population in a host, and these variations may contribute to the best fit of the CTV in different situations. In Iran, whole genome sequencing of the CTV was performed for the first time, and we gained new insights into CTV variation in a population.
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Affiliation(s)
- Abozar Ghorbani
- Nuclear Science and Technology Research Institute, Nuclear Agriculture Research School, Karaj, Iran
| | - Mohammad Mehdi Faghihi
- Plant Protection Research Department, Fars Agricultural and Natural Resources Research and Education Centre, AREEO, Zarghan, Iran
| | - Faezeh Falaki
- Department of Plant Protection, College of Agriculture Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran
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3
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Aknadibossian V, Huguet-Tapia JC, Golyaev V, Pooggin MM, Folimonova SY. Transcriptomic alterations in the sweet orange vasculature correlate with growth repression induced by a variant of citrus tristeza virus. Front Microbiol 2023; 14:1162613. [PMID: 37138615 PMCID: PMC10150063 DOI: 10.3389/fmicb.2023.1162613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
Citrus tristeza virus (CTV, family Closteroviridae) is an economically important pathogen of citrus. CTV resides in the phloem of the infected plants and induces a range of disease phenotypes, including stem pitting and quick decline as well as a number of other deleterious syndromes. To uncover the biological processes underlying the poorly understood damaging symptoms of CTV, we profiled the transcriptome of sweet orange (Citrus sinensis) phloem-rich bark tissues of non-infected, mock-inoculated trees and trees singly infected with two distinct variants of CTV, T36 or T68-1. The T36 and T68-1 variants accumulated in the infected plants at similar titers. With that, young trees infected with T68-1 were markedly repressed in growth, while the growth rate of the trees infected with T36 was comparable to the mock-inoculated trees. Only a small number of differentially expressed genes (DEGs) were identified in the nearly asymptomatic T36-infected trees, whereas almost fourfold the number of DEGs were identified with the growth-restricting T68-1 infection. DEGs were validated using quantitative reverse transcription-PCR. While T36 did not induce many noteworthy changes, T68-1 altered the expression of numerous host mRNAs encoding proteins within significant biological pathways, including immunity and stress response proteins, papain-like cysteine proteases (PLCPs), cell-wall modifying enzymes, vascular development proteins and others. The transcriptomic alterations in the T68-1-infected trees, in particular, the strong and persistent increase in the expression levels of PLCPs, appear to contribute to the observed stem growth repression. On the other hand, analysis of the viral small interfering RNAs revealed that the host RNA silencing-based response to the infection by T36 and that by T68-1 was comparable, and thus, the induction of this antiviral mechanism may not contribute to the difference in the observed symptoms. The DEGs identified in this study promote our understanding of the underlying mechanisms of the yet unexplained growth repression induced by severe CTV isolates in sweet orange trees.
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Affiliation(s)
- Vicken Aknadibossian
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Victor Golyaev
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, IRD, Institute Agro, Montpellier, France
| | - Mikhail M. Pooggin
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, IRD, Institute Agro, Montpellier, France
| | - Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
- *Correspondence: Svetlana Y. Folimonova,
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4
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Folimonova SY, Sun YD. Citrus Tristeza Virus: From Pathogen to Panacea. Annu Rev Virol 2022; 9:417-435. [DOI: 10.1146/annurev-virology-100520-114412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Citrus tristeza virus (CTV) is the most destructive viral pathogen of citrus. During the past century, CTV induced grave epidemics in citrus-growing areas worldwide that have resulted in a loss of more than 100 million trees. At present, the virus continues to threaten citrus production in many different countries. Research on CTV is accompanied by distinctive challenges stemming from the large size of its RNA genome, the narrow host range limited to slow-growing Citrus species and relatives, and the complexity of CTV populations. Despite these hurdles, remarkable progress has been made in understanding the CTV-host interactions and in converting the virus into a tool for crop protection and improvement. This review focuses on recent advances that have shed light on the mechanisms underlying CTV infection. Understanding these mechanisms is pivotal for the development of means to control CTV diseases and, ultimately, turn this virus into an ally. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, USA
| | - Yong-Duo Sun
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Ghosh DK, Kokane A, Kokane S, Mukherjee K, Tenzin J, Surwase D, Deshmukh D, Gubyad M, Biswas KK. A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World. Front Microbiol 2022; 13:797463. [PMID: 35464978 PMCID: PMC9024366 DOI: 10.3389/fmicb.2022.797463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.
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Affiliation(s)
- Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
- *Correspondence: Dilip Kumar Ghosh,
| | - Amol Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Sunil Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Krishanu Mukherjee
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
| | - Jigme Tenzin
- National Citrus Program, Department of Agriculture, Royal Government of Bhutan, Thimpu, Bhutan
| | - Datta Surwase
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Dhanshree Deshmukh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Mrugendra Gubyad
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, India
| | - Kajal Kumar Biswas
- Department of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Moreno P, López C, Ruiz-Ruiz S, Peña L, Guerri J. From the smallest to the largest subcellular plant pathogen: Citrus tristeza virus and its unique p23 protein. Virus Res 2022; 314:198755. [PMID: 35341876 DOI: 10.1016/j.virusres.2022.198755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
Abstract
Knowledge on diseases caused by Citrus tristeza virus (CTV) has greatly increased in last decades after their etiology was demonstrated in the past seventies. Professor Ricardo Flores substantially contributed to these advances in topics like: i) improvement of virus purification to obtain biologically active virions, ii) sequencing mild CTV isolates for genetic comparisons with sequences of moderate or severe isolates and genetic engineering, iii) analysis of genetic variation of both CTV genomic RNA ends and features of the highly variable 5' end that allow accommodating this variation within a conserved secondary structure, iv) studies on the structure, subcellular localization and biological functions of the CTV-unique p23 protein, and v) potential use of p23 and other 3'-proximal regions of the CTV genome to develop transgenic citrus resistant to the virus. Here we review his main achievements on these topics and how they contributed to deeper understanding of CTV biology and to new potential measures for disease control.
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Affiliation(s)
- Pedro Moreno
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113-Valencia, Spain. (Retired).
| | - Carmelo López
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, 46022-Valencia, Spain
| | - Susana Ruiz-Ruiz
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46022-Valencia, Spain
| | - Leandro Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), 46022-Valencia, Spain
| | - José Guerri
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113-Valencia, Spain. (Retired)
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7
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Sun YD, Folimonova SY. Location matters: from changing a presumption about the Citrus tristeza virus tissue tropism to understanding the stem pitting disease. THE NEW PHYTOLOGIST 2022; 233:631-638. [PMID: 34614233 DOI: 10.1111/nph.17777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Stem pitting is a common virus-induced disease phenotype that tremendously impacts growth of perennial woody plants. How stem pitting develops in the infected trees remains unclear. Here, we assessed the development of stem pits upon infection of citrus by Citrus tristeza virus (CTV), which has been regarded as 'phloem-limited'. By taking advantage of a highly susceptible virus host - Citrus macrophylla - and a CTV isolate lacking a viral effector - the p33 protein, the development pattern of stem pitting was revealed via time-course observations and histological analyses. The stem pits result from the virus-colonized nonlignified 'gumming' malformations which are initiated by virus invasion into multiple spatially separated tissue layers - protophloem, metaphloem, and, unexpectedly, metaxylem. Notably, invasion of CTV into the unspecialized metaxylem cells interrupted the differentiation of the xylem tracheary elements. With the radial spread of CTV into the adjacent cells towards the stem periphery, the clusters of virus-colonized immature metaxylem cells extended in size, merging, at a certain stage, with virus-bearing cells in the protophloem and metaphloem layers. Collectively, our data provide a new insight into the process of the stem pitting development and the role of the xylem tissue in the virus pathogenicity.
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Affiliation(s)
- Yong-Duo Sun
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
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8
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Kang SH, Aknadibossian V, Kharel L, Mudiyanselage SDD, Wang Y, Folimonova SY. The Intriguing Conundrum of a Nonconserved Multifunctional Protein of Citrus Tristeza Virus That Interacts with a Viral Long Non-Coding RNA. Viruses 2021; 13:2129. [PMID: 34834936 PMCID: PMC8625556 DOI: 10.3390/v13112129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Citrus tristeza virus (CTV), the largest non-segmented plant RNA virus, has several peculiar features, among which is the production of a 5'-terminal long non-coding RNA (lncRNA) termed low-molecular-weight tristeza 1 (LMT1). In this study, we found that p33, a unique viral protein that performs multiple functions in the virus infection cycle, specifically binds LMT1, both in vivo and in vitro. These results were obtained through the expression of p33 under the context of the wild type virus infection or along with a mutant CTV variant that does not produce LMT1 as well as via ectopic co-expression of p33 with LMT1 in Nicotiana benthamiana leaves followed by RNA immunoprecipitation and rapid amplification of cDNA ends assays. Further experiments in which a recombinant p33 protein and an in vitro transcribed full-length LMT1 RNA or its truncated fragments were subjected to an electrophoretic mobility shift assay demonstrated that p33 binds to at least two distinct regions within LMT1. To the best of our knowledge, this is the first report of a plant virus protein binding to a lncRNA produced by the same virus. The biological significance of the interaction between these two viral factors is discussed.
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Affiliation(s)
- Sung-Hwan Kang
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (S.-H.K.); (V.A.)
| | - Vicken Aknadibossian
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (S.-H.K.); (V.A.)
| | - Laxmi Kharel
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; (L.K.); (S.D.D.M.); (Y.W.)
| | | | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; (L.K.); (S.D.D.M.); (Y.W.)
| | - Svetlana Y. Folimonova
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (S.-H.K.); (V.A.)
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Development of a real-time RT-PCR method for the detection of Citrus tristeza virus (CTV) and its implication in studying virus distribution in planta. 3 Biotech 2021; 11:431. [PMID: 34603909 DOI: 10.1007/s13205-021-02976-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022] Open
Abstract
Tristeza is an economically important disease of the citrus caused by Citrus tristeza virus (CTV) of genus Closterovirus and family Closteroviridae. The disease has caused tremendous losses to citrus industry worldwide by killing millions of trees, reducing the productivity and total production. Enormous efforts have been made in many countries to prevent the viral spread and the losses caused by the disease. To understand the reason behind this scenario, studies on virus distribution and tropism in the citrus plants are needed. Different diagnostic methods are available for early CTV detection but none of them is employed for in planta virus distribution study. In this study, a TaqMan RT-PCR-based method to detect and quantify CTV in different tissues of infected Mosambi plants (Citrus sinensis) has been standardized. The assay was very sensitive with the pathogen detection limit of > 0.0595 fg of in vitro-transcribed CTV-RNA. The assay was implemented for virus distribution study and absolute CTV titer quantification in samples taken from Tristeza-infected trees. The highest virus load was observed in the midribs of the symptomatic leaf (4.1 × 107-1.4 × 108/100 mg) and the lowest in partial dead twigs (1 × 103-1.7 × 104/100 mg), and shoot tip (2.3 × 103-4.5 × 103/100 mg). Interestingly, during the peak summer months, the highest CTV load was observed in the feeder roots (3 × 107-1.1 × 108/100 mg) than in the midribs of symptomatic leaf. The viral titer was highest in symptomatic leaf midrib followed by asymptomatic leaf midrib, feeder roots, twig bark, symptomatic leaf lamella, and asymptomatic leaf lamella. Overall, high CTV titer was primarily observed in the phloem containing tissues and low CTV titer in the other tissues. The information would help in selecting tissues with higher virus titer in disease surveillance that have implication in Tristeza management in citrus.
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Liu Q, Zhang S, Mei S, Zhou Y, Wang J, Han GZ, Chen L, Zhou C, Cao M. Viromics unveils extraordinary genetic diversity of the family Closteroviridae in wild citrus. PLoS Pathog 2021; 17:e1009751. [PMID: 34252150 PMCID: PMC8297929 DOI: 10.1371/journal.ppat.1009751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/22/2021] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
Our knowledge of citrus viruses is largely skewed toward virus pathology in cultivated orchards. Little is known about the virus diversity in wild citrus species. Here, we used a metatranscriptomics approach to characterize the virus diversity in a wild citrus habitat within the proposed center of the origin of citrus plants. We discovered a total of 44 virus isolates that could be classified into species Citrus tristeza virus and putative species citrus associated ampelovirus 1, citrus associated ampelovirus 2, and citrus virus B within the family Closteroviridae, providing important information to explore the factors facilitating outbreaks of citrus viruses and the evolutionary history of the family Closteroviridae. We found that frequent horizontal gene transfer, gene duplication, and alteration of expression strategy have shaped the genome complexity and diversification of the family Closteroviridae. Recombination frequently occurred among distinct Closteroviridae members, thereby facilitating the evolution of Closteroviridae. Given the potential emergence of similar wild-citrus-originated novel viruses as pathogens, the need for surveillance of their pathogenic and epidemiological characteristics is of utmost priority for global citrus production. Closterovirids are principal plant pathogens for citrus trees and other plants, as they sometimes cause new or re-emerging diseases. However, the closterovirid diversity in natural plant hosts, especially citrus plants, is unclear. Here, we describe three novel species and Citrus tristeza virus within the family Closteroviridae that were sampled from wild citrus trees growing in their natural habitat in southwestern China. The presence of three different taxon classes of the family Closteroviridae indicates the geographical uniqueness of the sampling region for citrus closterovirid evolution. Our analysis shows that frequent horizontal gene transfer, gene duplication, alteration of expression strategy, and recombination have been important evolutionary processes in the diversification of the family Closteroviridae. Our study also shows the significance of natural reserves as potential sources of disease agents endangering cultivated crop plants.
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Affiliation(s)
- Qiyan Liu
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, China
| | - Shiqiang Mei
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, China
| | - Yan Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, China
| | - Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Lei Chen
- Industrial Crop Workstation of Xinping County, Yuxi, Yunnan, China
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, China
- * E-mail: (CZ); (MC)
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, China
- * E-mail: (CZ); (MC)
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11
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Ambrós S, Gómez-Muñoz N, Giménez-Santamarina S, Sánchez-Vicente J, Navarro-López J, Martínez F, Daròs JA, Rodrigo G. Molecular signatures of silencing suppression degeneracy from a complex RNA virus. PLoS Comput Biol 2021; 17:e1009166. [PMID: 34181647 PMCID: PMC8270454 DOI: 10.1371/journal.pcbi.1009166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/09/2021] [Accepted: 06/09/2021] [Indexed: 11/21/2022] Open
Abstract
As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA silencing suppressors, using an experimental system of transient expression in a model plant. The study was expanded by considering two different isolates of the virus, and some key interactions were confirmed by bimolecular fluorescence complementation assays. We found that p20 and p25 target a common set of plant proteins including chloroplastic proteins and translation factors. Moreover, we noted that even specific targets of each viral protein overlap in function. Notably, we identified argonaute proteins (key players in RNA silencing) as reliable targets of p20. Furthermore, we found that these viral proteins preferentially do not target hubs in the host protein interactome, but elements that can transfer information by bridging different parts of the interactome. Overall, our results demonstrate that two distinct proteins encoded in the same viral genome that overlap in function also overlap in their interactions with the cell proteome, thereby highlighting an overlooked connection from a degenerate viral system.
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Affiliation(s)
- Silvia Ambrós
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC–Universitat Politècnica de València, València, Spain
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC–Universitat de València, Paterna, Spain
| | - Neus Gómez-Muñoz
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Silvia Giménez-Santamarina
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC–Universitat Politècnica de València, València, Spain
| | - Javier Sánchez-Vicente
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC–Universitat Politècnica de València, València, Spain
| | - Josep Navarro-López
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC–Universitat Politècnica de València, València, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC–Universitat Politècnica de València, València, Spain
| | - Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC–Universitat Politècnica de València, València, Spain
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC–Universitat de València, Paterna, Spain
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12
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Sun Y, Zhang L, Folimonova SY. Citrus miraculin-like protein hijacks a viral movement-related p33 protein and induces cellular oxidative stress in defence against Citrus tristeza virus. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:977-991. [PMID: 33283396 PMCID: PMC8131049 DOI: 10.1111/pbi.13523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/26/2020] [Accepted: 11/30/2020] [Indexed: 05/16/2023]
Abstract
To defend against pathogens, plants have developed a complex immune system, which recognizes the pathogen effectors and mounts defence responses. In this study, the p33 protein of Citrus tristeza virus (CTV), a viral membrane-associated effector, was used as a molecular bait to explore virus interactions with host immunity. We discovered that Citrus macrophylla miraculin-like protein 2 (CmMLP2), a member of the soybean Kunitz-type trypsin inhibitor family, targets the viral p33 protein. The expression of CmMLP2 was up-regulated by p33 in the citrus phloem-associated cells. Knock-down of the MLP2 expression in citrus plants resulted in a higher virus accumulation, while the overexpression of CmMLP2 reduced the infectivity of CTV in the plant hosts. Further investigation revealed that, on the one hand, binding of CmMLP2 interrupts the cellular distribution of p33 whose proper function is necessary for the effective virus movement throughout the host. On the other hand, the ability of CmMLP2 to reorganize the endomembrane system, amalgamating the endoplasmic reticulum and the Golgi apparatus, induces cellular stress and accumulation of the reactive oxygen species, which inhibits the replication of CTV. Altogether, our data suggest that CmMLP2 employs a two-way strategy in defence against CTV infection.
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Affiliation(s)
- Yong‐Duo Sun
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
| | - Lei Zhang
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
- Present address:
College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhot010018China
| | - Svetlana Y. Folimonova
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
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13
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Bester R, Cook G, Maree HJ. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses 2021; 13:168. [PMID: 33498597 PMCID: PMC7910887 DOI: 10.3390/v13020168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa;
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Citrus Research International, Stellenbosch, P.O. Box 2201, Matieland 7602, South Africa
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14
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Gao Z, Pu H, Liu J, Wang X, Zhong C, Yue N, Zhang Z, Wang XB, Han C, Yu J, Li D, Zhang Y. Tobacco Necrosis Virus-A C Single Coat Protein Amino Acid Substitutions Determine Host-Specific Systemic Infections of Nicotiana benthamiana and Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:49-61. [PMID: 32986512 DOI: 10.1094/mpmi-07-20-0184-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plant viruses often infect several distinct host species. Sometimes, viruses can systemically infect a specific host whereas, in other cases, only local infections occur in other species. How viral and host factors interact to determine systemic infections among different hosts is largely unknown, particularly for icosahedral positive-stranded RNA viruses. The Tobacco necrosis virus-A Chinese isolate belongs to the genus Alphanecrovirus in the family Tombusviridae. In this study, we investigated variations in systemic infections of tobacco necrosis virus-AC (TNV-AC) in Nicotiana benthamiana and Glycine max (soybean) by alanine-scanning mutagenesis of the viral coat protein (CP), which is essential for systemic movement of TNV-AC. We found that three amino acids, R169, K177, and Q233, are key residues that mediate varying degrees of systemic infections of N. benthamiana and soybean. Further analysis revealed that variations in systemic trafficking of TNV-AC CP mutants in N. benthamiana and soybean are associated with virion assembly and stability. The CP amino acids K177 and Q233 are highly conserved among all TNV-A isolates and are replaced by Q and K in the TNV-D isolates. We demonstrated that systemic infectivity of either TNV-AC K177A and Q233A or K177Q and Q233K mutants are correlated with the binding affinity of the mutated CPs to the host-specific Hsc70-2 protein. These results expand our understanding of host-dependent long-distance movement of icosahedral viruses in plants.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zongyu Gao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Heng Pu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Jingyuan Liu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Xiaoling Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Chenchen Zhong
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Ning Yue
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Ziding Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
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15
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Chen AYS, Peng JHC, Polek M, Tian T, Ludman M, Fátyol K, Ng JCK. Comparative analysis identifies amino acids critical for citrus tristeza virus (T36CA) encoded proteins involved in suppression of RNA silencing and differential systemic infection in two plant species. MOLECULAR PLANT PATHOLOGY 2021; 22:64-76. [PMID: 33118689 PMCID: PMC7749750 DOI: 10.1111/mpp.13008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 05/06/2023]
Abstract
Complementary (c)DNA clones corresponding to the full-length genome of T36CA (a Californian isolate of Citrus tristeza virus with the T36 genotype), which shares 99.1% identity with that of T36FL (a T36 isolate from Florida), were made into a vector system to express the green fluorescent protein (GFP). Agroinfiltration of two prototype T36CA-based vectors (pT36CA) to Nicotiana benthamiana plants resulted in local but not systemic GFP expression/viral infection. This contrasted with agroinfiltration of the T36FL-based vector (pT36FL), which resulted in both local and systemic GFP expression/viral infection. A prototype T36CA systemically infected RNA silencing-defective N. benthamiana lines, demonstrating that a genetic basis for its defective systemic infection was RNA silencing. We evaluated the in planta bioactivity of chimeric pT36CA-pT36FL constructs and the results suggested that nucleotide variants in several open reading frames of the prototype T36CA could be responsible for its defective systemic infection. A single amino acid substitution in each of two silencing suppressors, p20 (S107G) and p25 (G36D), of prototype T36CA facilitated its systemic infectivity in N. benthamiana (albeit with reduced titre relative to that of T36FL) but not in Citrus macrophylla plants. Enhanced virus accumulation and, remarkably, robust systemic infection of T36CA in N. benthamiana and C. macrophylla plants, respectively, required two additional amino acid substitutions engineered in p65 (N118S and S158L), a putative closterovirus movement protein. The availability of pT36CA provides a unique opportunity for comparative analysis to identify viral coding and noncoding nucleotides or sequences involved in functions that are vital for in planta infection.
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Affiliation(s)
- Angel Y. S. Chen
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - James H. C. Peng
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - MaryLou Polek
- National Clonal Germplasm Repository for Citrus & DatesUSDA ARSRiversideCaliforniaUSA
| | - Tongyan Tian
- California Department of Food and AgricultureSacramentoCaliforniaUSA
| | - Márta Ludman
- Agricultural Biotechnology InstituteNational Research and Innovation CenterHungary
| | - Károly Fátyol
- Agricultural Biotechnology InstituteNational Research and Innovation CenterHungary
| | - James C. K. Ng
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
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16
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Walking Together: Cross-Protection, Genome Conservation, and the Replication Machinery of Citrus tristeza virus. Viruses 2020; 12:v12121353. [PMID: 33256049 PMCID: PMC7760907 DOI: 10.3390/v12121353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/25/2020] [Indexed: 01/23/2023] Open
Abstract
"Cross-protection", a nearly 100 years-old virological term, is suggested to be changed to "close protection". Evidence for the need of such change has accumulated over the past six decades from the laboratory experiments and field tests conducted by plant pathologists and plant virologists working with different plant viruses, and, in particular, from research on Citrus tristeza virus (CTV). A direct confirmation of such close protection came with the finding that "pre-immunization" of citrus plants with the variants of the T36 strain of CTV but not with variants of other virus strains was providing protection against a fluorescent protein-tagged T36-based recombinant virus variant. Under natural conditions close protection is functional and is closely associated both with the conservation of the CTV genome sequence and prevention of superinfection by closely similar isolates. It is suggested that the mechanism is primarily directed to prevent the danger of virus population collapse that could be expected to result through quasispecies divergence of large RNA genomes of the CTV variants continuously replicating within long-living and highly voluminous fruit trees. This review article provides an overview of the CTV cross-protection research, along with a discussion of the phenomenon in the context of the CTV biology and genetics.
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17
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Panstruga R, Moscou MJ. What is the Molecular Basis of Nonhost Resistance? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1253-1264. [PMID: 32808862 DOI: 10.1094/mpmi-06-20-0161-cr] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term "nonhost genes" is misleading and should be avoided. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view of plant immunity.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringer Weg 1, 52056 Aachen, Germany
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, United Kingdom
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18
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Shilts T, El-Mohtar C, Dawson WO, Killiny N. Citrus tristeza virus P33 Protein is Required for Efficient Transmission by the Aphid Aphis ( Toxoptera) citricidus (Kirkaldy). Viruses 2020; 12:E1131. [PMID: 33036216 PMCID: PMC7600554 DOI: 10.3390/v12101131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 12/24/2022] Open
Abstract
Plant viruses are threatening many valuable crops, and Citrus tristeza virus (CTV) is considered one of the most economically important plant viruses. CTV has destroyed millions of citrus trees in many regions of the world. Consequently, understanding of the transmission mechanism of CTV by its main vector, the brown citrus aphid, Aphis (Toxoptera) citricidus (Kirkaldy), may lead to better control strategies for CTV. The objective of this study was to understand the CTV-vector relationship by exploring the influence of viral genetic diversity on virus transmission. We built several infectious clones with different 5'-proximal ends from different CTV strains and assessed their transmission by the brown citrus aphid. Replacement of the 5'- end of the T36 isolate with that of the T30 strain (poorly transmitted) did not increase the transmission rate of T36, whereas replacement with that of the T68-1 isolate (highly transmitted) increased the transmission rate of T36 from 1.5 to 23%. Finally, substitution of p33 gene of the T36 strain with that of T68 increased the transmission rate from 1.5% to 17.8%. Although the underlying mechanisms that regulate the CTV transmission process by aphids have been explored in many ways, the roles of specific viral proteins are still not explicit. Our findings will improve our understanding of the transmission mechanisms of CTV by its aphid vector and may lead to the development of control strategies that interfere with its transmission by vector.
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Affiliation(s)
| | | | | | - Nabil Killiny
- Plant Pathology Department, CREC-IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA; (T.S.); (C.E.-M.); (W.O.D.)
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19
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Davino S, Ruiz-Ruiz S, Serra P, Forment J, Flores R. Revisiting the cysteine-rich proteins encoded in the 3'-proximal open reading frame of the positive-sense single-stranded RNA of some monopartite filamentous plant viruses: functional dissection of p15 from grapevine virus B. Arch Virol 2020; 165:2229-2239. [PMID: 32676682 DOI: 10.1007/s00705-020-04729-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/09/2020] [Indexed: 10/23/2022]
Abstract
A reexamination of proteins with conserved cysteines and basic amino acids encoded by the 3'-proximal gene of the positive-sense single-stranded RNA of some monopartite filamentous plant viruses has been carried out. The cysteines are involved in a putative Zn-finger domain, which, together with the basic amino acids, form part of the nuclear or nucleolar localization signals. An in-depth study of one of these proteins, p15 from grapevine B virus (GVB), has shown: (i) a three-dimensional structure with four α-helices predicted by two independent in silico approaches, (ii) the nucleolus as the main accumulation site by applying confocal laser microscopy to a fusion between p15 and the green fluorescent protein, (iii) the involvement of the basic amino acids and the putative Zn-finger domain, mapping at the N-terminal region of p15, in the nucleolar localization signal, as revealed by the effect of six alanine substitution mutations, (iv) the p15 suppressor function of sense-mediated RNA silencing as revealed by agroinfiltration in a transgenic line of Nicotiana benthamiana, and (v) the enhancer activity of p15 on viral pathogenicity in N. benthamiana when expressed from a potato virus X vector. In addition, we elaborate on an evolutionary scenario for these filamentous viruses, invoking takeover by a common ancestor(s) of viral or host genes coding for those cysteine-rich proteins, followed by divergence, which would also explain why they are encoded in the 3'-proximal gene of the genomic single-stranded viral RNA.
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Affiliation(s)
- Salvatore Davino
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022, Valencia, Spain
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze Building 5, 90128, Palermo, Italy
| | - Susana Ruiz-Ruiz
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022, Valencia, Spain
| | - Pedro Serra
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022, Valencia, Spain
| | - Javier Forment
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022, Valencia, Spain
| | - Ricardo Flores
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022, Valencia, Spain.
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20
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Sanfaçon H. Modulation of disease severity by plant positive-strand RNA viruses: The complex interplay of multifunctional viral proteins, subviral RNAs and virus-associated RNAs with plant signaling pathways and defense responses. Adv Virus Res 2020; 107:87-131. [PMID: 32711736 DOI: 10.1016/bs.aivir.2020.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant viruses induce a range of symptoms of varying intensity, ranging from severe systemic necrosis to mild or asymptomatic infection. Several evolutionary constraints drive virus virulence, including the dependence of viruses on host factors to complete their infection cycle, the requirement to counteract or evade plant antiviral defense responses and the mode of virus transmission. Viruses have developed an array of strategies to modulate disease severity. Accumulating evidence has highlighted not only the multifunctional role that viral proteins play in disrupting or highjacking plant factors, hormone signaling pathways and intracellular organelles, but also the interaction networks between viral proteins, subviral RNAs and/or other viral-associated RNAs that regulate disease severity. This review focusses on positive-strand RNA viruses, which constitute the majority of characterized plant viruses. Using well-characterized viruses with different genome types as examples, recent advances are discussed as well as knowledge gaps and opportunities for further research.
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Affiliation(s)
- Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada.
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21
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Dao TNM, Kang SH, Bak A, Folimonova SY. A Non-Conserved p33 Protein of Citrus Tristeza Virus Interacts with Multiple Viral Partners. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:859-870. [PMID: 32141354 DOI: 10.1094/mpmi-11-19-0328-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The RNA genome of citrus tristeza virus (CTV), one of the most damaging viral pathogens of citrus, contains 12 open reading frames resulting in production of at least 19 proteins. Previous studies on the intraviral interactome of CTV revealed self-interaction of the viral RNA-dependent RNA polymerase, the major coat protein (CP), p20, p23, and p33 proteins, while heterologous interactions between the CTV proteins have not been characterized. In this work, we examined interactions between the p33 protein, a nonconserved protein of CTV, which performs multiple functions in the virus infection cycle and is needed for virus ability to infect the extended host range, with other CTV proteins shown to mediate virus interactions with its plant hosts. Using yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays, we demonstrated that p33 interacts with three viral proteins, i.e., CP, p20, and p23, in vivo and in planta. Coexpression of p33, which is an integral membrane protein, resulted in a shift in the localization of the p20 and p23 proteins toward the subcellular crude-membrane fraction. Upon CTV infection, the four proteins colocalized in the CTV replication factories. In addition, three of them, CP, p20, and p23, were found in the p33-formed membranous structures. Using bioinformatic analyses and mutagenesis, we found that the N-terminus of p33 is involved in the interactions with all three protein partners. A potential role of these interactions in virus ability to infect the extended host range is discussed.
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Affiliation(s)
- Thi Nguyet Minh Dao
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, U.S.A
| | - Sung-Hwan Kang
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, U.S.A
| | - Aurélie Bak
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, U.S.A
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22
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Moury B, Desbiez C. Host Range Evolution of Potyviruses: A Global Phylogenetic Analysis. Viruses 2020; 12:v12010111. [PMID: 31963241 PMCID: PMC7020010 DOI: 10.3390/v12010111] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022] Open
Abstract
Virus host range, i.e., the number and diversity of host species of viruses, is an important determinant of disease emergence and of the efficiency of disease control strategies. However, for plant viruses, little is known about the genetic or ecological factors involved in the evolution of host range. Using available genome sequences and host range data, we performed a phylogenetic analysis of host range evolution in the genus Potyvirus, a large group of plant RNA viruses that has undergone a radiative evolution circa 7000 years ago, contemporaneously with agriculture intensification in mid Holocene. Maximum likelihood inference based on a set of 59 potyviruses and 38 plant species showed frequent host range changes during potyvirus evolution, with 4.6 changes per plant species on average, including 3.1 host gains and 1.5 host loss. These changes were quite recent, 74% of them being inferred on the terminal branches of the potyvirus tree. The most striking result was the high frequency of correlated host gains occurring repeatedly in different branches of the potyvirus tree, which raises the question of the dependence of the molecular and/or ecological mechanisms involved in adaptation to different plant species.
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23
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Abstract
Strategies to manage plant disease-from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences-all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant-microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum-more so than the separation of discrete pathotypes-and that host jumps are common. By setting the mechanisms of plant-pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.
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Affiliation(s)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140, Montfavet, France;
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24
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Kang SH, Sun YD, Atallah OO, Huguet-Tapia JC, Noble JD, Folimonova SY. A Long Non-Coding RNA of Citrus tristeza virus: Role in the Virus Interplay with the Host Immunity. Viruses 2019; 11:E436. [PMID: 31091710 PMCID: PMC6563247 DOI: 10.3390/v11050436] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 01/01/2023] Open
Abstract
During infection, Citrus tristeza virus (CTV) produces a non-coding subgenomic RNA referred to as low-molecular-weight tristeza 1 (LMT1), which for a long time has been considered as a by-product of the complex CTV replication machinery. In this study, we investigated the role of LMT1 in the virus infection cycle using a CTV variant that does not produce LMT1 (CTV-LMT1d). We showed that lack of LMT1 did not halt virus ability to replicate or form proper virions. However, the mutant virus demonstrated significantly reduced invasiveness and systemic spread in Nicotiana benthamiana as well as an inability to establish infection in citrus. Introduction of CTV-LMT1d into the herbaceous host resulted in elevation of the levels of salicylic acid (SA) and SA-responsive pathogenesis-related genes beyond those upon inoculation with wild-type (WT) virus (CTV-WT). Further analysis showed that the LMT1 RNA produced by CTV-WT or via ectopic expression in the N. benthamiana leaves suppressed SA accumulation and up-regulated an alternative oxidase gene, which appeared to mitigate the accumulation of reactive oxygen species. To the best of our knowledge, this is the first report of a plant viral long non-coding RNA being involved in counter-acting host response by subverting the SA-mediated plant defense.
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Affiliation(s)
- Sung-Hwan Kang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Yong-Duo Sun
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - Osama O Atallah
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | | | - Jerald D Noble
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - Svetlana Y Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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Sun YD, Folimonova SY. The p33 protein of Citrus tristeza virus affects viral pathogenicity by modulating a host immune response. THE NEW PHYTOLOGIST 2019; 221:2039-2053. [PMID: 30220089 DOI: 10.1111/nph.15482] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
Accumulation of reactive oxygen species (ROS) is a general plant basal defense strategy against viruses. In this study, we show that infection by Citrus tristeza virus (CTV) triggered ROS burst in Nicotiana benthamiana and in the natural citrus host, the extent of which was virus-dose dependent. Using Agrobacterium-mediated expression of CTV-encoded proteins in N. benthamiana, we found that p33, a unique viral protein, contributed to the induction of ROS accumulation and programmed cell death. The role of p33 in CTV pathogenicity was assessed based on gene knockout and complementation in N. benthamiana. In the citrus-CTV pathosystem, deletion of the p33 open reading frame in a CTV variant resulted in a significant decrease in ROS production, compared to that of the wild type CTV, which correlated with invasion of the mutant virus into the immature xylem tracheid cells and abnormal differentiation of the vascular system. By contrast, the wild type CTV exhibited phloem-limited distribution with a minor effect on the vasculature. We conclude that the p33 protein is a CTV effector that negatively affects virus pathogenicity and suggest that N. benthamiana recognizes p33 to activate the host immune response to restrict CTV into the phloem tissue and minimize the disease syndrome.
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Affiliation(s)
- Yong-Duo Sun
- Plant Pathology Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Folimonova
- Plant Pathology Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
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Ruiz-Ruiz S, Navarro B, Peña L, Navarro L, Moreno P, Di Serio F, Flores R. Citrus tristeza virus: Host RNA Silencing and Virus Counteraction. Methods Mol Biol 2019; 2015:195-207. [PMID: 31222705 DOI: 10.1007/978-1-4939-9558-5_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To dissect the host RNA silencing response incited by citrus tristeza virus (CTV, genus Closterovirus), a (+) ssRNA of ~19300 nt, and the counter reaction deployed by the virus via its three RNA silencing suppressors (RSS), the small RNAs (sRNAs) of three virus-host combinations were deep sequenced. The subsequent analysis indicated that CTV sRNAs (1) constitute more than half of the total sRNAs in the susceptible Mexican lime and sweet orange, while only 3.5% in the restrictive sour orange; (2) are mostly of 21-22 nt, with those of (+) sense predominating slightly; and (3) derive from all the CTV genome, as evidenced by its entire recomposition from viral sRNA contigs but adopt an asymmetric pattern with a hotspot mapping at the 3'-terminal ~2500 nt. The citrus homologues of Arabidopsis Dicer-like (DCL) 4 and 2 most likely generate the 21 and 22 nt CTV sRNAs, respectively, by dicing the gRNA and the 3' co-terminal sgRNAs and, particularly, their double-stranded forms accumulating in infected cells. The plant sRNA profile, very similar and dominated by the 24 nt sRNAs in the three mock-inoculated controls, displayed a major reduction of the 24 nt sRNAs in Mexican lime and sweet orange, but not in sour orange. CTV infection also influences the levels of certain microRNAs.The high accumulation of CTV sRNAs in two of the citrus hosts examined suggests that it is not their synthesis, but their function, the target of the RSS encoded by CTV: p25 (intercellular), p23 (intracellular) and p20 (both). The two latter might block the loading of CTV sRNAs into the RNA silencing complex or interfere with it through alternative mechanisms. Of the three CTV RSS, p23 is the one that has been more thoroughly studied. It is a multifunctional RNA-binding protein with a putative Zn finger domain and basic motifs that (1) has no homologues in other closteroviruses, (2) accumulates in the nucleolus and plasmodesmata, (3) regulates the asymmetric balance of CTV (+) and (-) RNA strands, and (4) induces CTV syndromes and stimulates systemic infection in certain citrus species when expressed as a transgene ectopically or in phloem-associated cells.
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Affiliation(s)
- Susana Ruiz-Ruiz
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Leandro Peña
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pedro Moreno
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain.
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Scuderi G, Catara AF, Licciardello G. Genotyping Citrus tristeza virus Isolates by Sequential Multiplex RT-PCR and Microarray Hybridization in a Lab-on-Chip Device. Methods Mol Biol 2019; 2015:127-142. [PMID: 31222700 DOI: 10.1007/978-1-4939-9558-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus tristeza virus (CTV) is the largest known plant RNA virus (ca. 20 Kb), with a plethora of isolates conventionally categorized into six main genotypic groups (T36, VT, T3, RB, T68, T30). Each group includes many isolates with different phenotype profiles. Several techniques and protocols, mostly based on RT-PCR analysis of different regions of specific genes, have been developed for managing the diseases caused by CTV. However, more accurate genomic information would help to plan a correct strategy. This chapter describes a pilot protocol based on a sequential multiplex RT-PCR reaction and microarray hybridization in a miniaturized silicon lab-on-chip (LoC) device. The system comprises a set of 12 primers and 44 probes (× 2 replicates), designed on variable genomic regions of 6 genes: 5'UTR, ORF1a, ORF1b (RdRp), p33, p20, and p23. The system can rapidly analyze any genotype diversity associated with field isolates and distinguish the endemic from the non-endemic isolates. The identification of CTV strains is based on a number of probe hybridizations, which varies according to the genotypes present in the isolates and the differences among the genotypes.
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Affiliation(s)
| | - Antonino F Catara
- Formerly, Department of Phytosanitary Sciences, University of Catania, Catania, Italy
- Science and Technology Park of Sicily, Catania, Italy
| | - Grazia Licciardello
- Consiglio per la Ricerca in agricoltura e l'analisi dell'Economia Agraria (CREA), Centro di Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Acireale (Catania), Italy
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Nigam D, LaTourrette K, Souza PFN, Garcia-Ruiz H. Genome-Wide Variation in Potyviruses. FRONTIERS IN PLANT SCIENCE 2019; 10:1439. [PMID: 31798606 PMCID: PMC6863122 DOI: 10.3389/fpls.2019.01439] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/16/2019] [Indexed: 05/07/2023]
Abstract
Potyviruses (family Potyviridae, genus Potyvirus) are the result of an initial radiation event that occurred 6,600 years ago. The genus currently consists of 167 species that infect monocots or dicots, including domesticated and wild plants. Potyviruses are transmitted in a non-persistent way by more than 200 species of aphids. As indicated by their wide host range, worldwide distribution, and diversity of their vectors, potyviruses have an outstanding capacity to adapt to new hosts and environments. However, factors that confer adaptability are poorly understood. Viral RNA-dependent RNA polymerases introduce nucleotide substitutions that generate genetic diversity. We hypothesized that selection imposed by hosts and vectors creates a footprint in areas of the genome involved in host adaptation. Here, we profiled genomic and polyprotein variation in all species in the genus Potyvirus. Results showed that the potyviral genome is under strong negative selection. Accordingly, the genome and polyprotein sequence are remarkably stable. However, nucleotide and amino acid substitutions across the potyviral genome are not randomly distributed and are not determined by codon usage. Instead, substitutions preferentially accumulate in hypervariable areas at homologous locations across potyviruses. At a frequency that is higher than that of the rest of the genome, hypervariable areas accumulate non-synonymous nucleotide substitutions and sites under positive selection. Our results show, for the first time, that there is correlation between host range and the frequency of sites under positive selection. Hypervariable areas map to the N terminal part of protein P1, N and C terminal parts of helper component proteinase (HC-Pro), the C terminal part of protein P3, VPg, the C terminal part of NIb (RNA-dependent RNA polymerase), and the N terminal part of the coat protein (CP). Additionally, a hypervariable area at the NIb-CP junction showed that there is variability in the sequence of the NIa protease cleavage sites. Structural alignment showed that the hypervariable area in the CP maps to the N terminal flexible loop and includes the motif required for aphid transmission. Collectively, results described here show that potyviruses contain fixed hypervariable areas in key parts of the genome which provide mutational robustness and are potentially involved in host adaptation.
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Jarugula S, Gowda S, Dawson WO, Naidu RA. Development of infectious cDNA clones of Grapevine leafroll-associated virus 3 and analyses of the 5' non-translated region for replication and virion formation. Virology 2018; 523:89-99. [PMID: 30103103 DOI: 10.1016/j.virol.2018.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 01/28/2023]
Abstract
Infectious cDNA clones were developed for Grapevine leafroll-associated virus 3 (GLRaV-3, genus Ampelovirus, family Closteroviridae). In vitro RNA transcripts generated from cDNA clones showed replication via the production of 3'-coterminal subgenomic (sg) mRNAs in Nicotiana benthamiana protoplasts. The detection of sgRNAs and the recovery of progeny recombinant virions from N. benthamiana leaves agroinfiltrated with full-length cDNA clones confirmed RNA replication and virion formation. The 5' non-translated region (5' NTR) of GLRaV-3 was exchangeable between genetic variants and complement the corresponding cognate RNA functions in trans. Mutational analysis of the 5' NTR in minireplicon cDNA clones showed that the conserved 40 nucleotides at the 5'-terminus were indispensable for replication, compared to downstream variable portion of the 5' NTR. Some of the functional mutations in the 5' NTR were tolerated in full-length cDNA clones and produced sgRNAs and virions in N. benthamiana leaves, whereas other mutations affected replication and virion formation.
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Affiliation(s)
- Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, WA 99350, United States
| | - Siddarame Gowda
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - William O Dawson
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, WA 99350, United States.
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30
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Yue R, Lu C, Han X, Guo S, Yan S, Liu L, Fu X, Chen N, Guo X, Chi H, Tie S. Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection. BMC PLANT BIOLOGY 2018; 18:191. [PMID: 30208842 PMCID: PMC6136180 DOI: 10.1186/s12870-018-1419-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/06/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Maize rough dwarf disease (MRDD) is a severe disease that has been occurring frequently in southern China and many other Asian countries. MRDD is caused by the infection of Rice black streaked dwarf virus (RBSDV) and leads to significant economic losses in maize production. To well understand the destructive effects of RBSDV infection on maize growth, comparative proteomic analyses of maize seedlings under RBSDV infection was performed using an integrated approach involving LC-MS/MS and Tandem Mass Tag (TMT) labeling. RESULTS In total, 7615 maize proteins, 6319 of which were quantified. A total of 116 differentially accumulated proteins (DAPs) were identified, including 35 up- and 81 down-regulated proteins under the RBSDV infection. Enrichment analysis showed that the DAPs were most strongly associated with cyanoamino acid metabolism, protein processing in ER, and ribosome-related pathways. Two sulfur metabolism-related proteins were significantly reduced, indicating that sulfur may participate in the resistance against RBSDV infection. Furthermore, 15 DAPs involved in six metabolic pathways were identified in maize under the RBSDV infection. CONCLUSIONS Our data revealed that the responses of maize to RBSDV infection were controlled by various metabolic pathways.
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Affiliation(s)
- Runqing Yue
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Caixia Lu
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xiaohua Han
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Shulei Guo
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Shufeng Yan
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Lu Liu
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xiaolei Fu
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Nana Chen
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xinhai Guo
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Haifeng Chi
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Shuanggui Tie
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
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31
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Qiao W, Helpio EL, Falk BW. Two Crinivirus-Conserved Small Proteins, P5 and P9, Are Indispensable for Efficient Lettuce infectious yellows virus Infectivity in Plants. Viruses 2018; 10:E459. [PMID: 30154314 PMCID: PMC6163742 DOI: 10.3390/v10090459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 01/06/2023] Open
Abstract
Genomic analysis of Lettuce infectious yellows virus (LIYV) has revealed two short open reading frames (ORFs) on LIYV RNA2, that are predicted to encode a 5-kDa (P5) and a 9-kDa (P9) protein. The P5 ORF is part of the conserved quintuple gene block in the family Closteroviridae, while P9 orthologs are found in all Criniviruses. In this study, the expression of LIYV P5 and P9 proteins was confirmed; P5 is further characterized as an endoplasmic reticulum (ER)-localized integral transmembrane protein and P9 is a soluble protein. The knockout LIYV mutants presented reduced symptom severity and virus accumulation in Nicotiana benthamiana or lettuce plants, indicating their importance in efficient virus infection. The P5 mutant was successfully complemented by a dislocated P5 in the LIYV genome. The structural regions of P5 were tested and all were found to be required for the appropriate functions of P5. In addition, P5, as well as its ortholog P6, encoded by Citrus tristeza virus (CTV) and another ER-localized protein encoded by LIYV RNA1, were found to cause cell death when expressed in N. benthamiana plants from a TMV vector, and induce ER stress and the unfolded protein response (UPR).
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Affiliation(s)
- Wenjie Qiao
- Department of Plant Pathology, University of California, Davis, CA 95616, USA.
| | - Erin L Helpio
- Department of Plant Pathology, University of California, Davis, CA 95616, USA.
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, CA 95616, USA.
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Folimonova SY, Tilsner J. Hitchhikers, highway tolls and roadworks: the interactions of plant viruses with the phloem. CURRENT OPINION IN PLANT BIOLOGY 2018; 43:82-88. [PMID: 29476981 DOI: 10.1016/j.pbi.2018.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 05/24/2023]
Abstract
The phloem is of central importance to plant viruses, providing the route by which they spread throughout their host. Compared with virus movement in non-vascular tissue, phloem entry, exit, and long-distance translocation usually involve additional viral factors and complex virus-host interactions, probably, because the phloem has evolved additional protection against these molecular 'hitchhikers'. Recent progress in understanding phloem trafficking of endogenous mRNAs along with observations of membranous viral replication 'factories' in sieve elements challenge existing conceptions of virus long-distance transport. At the same time, the central role of the phloem in plant defences against viruses and the sophisticated viral manipulation of this host tissue are beginning to emerge.
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Affiliation(s)
| | - Jens Tilsner
- Biomedical Sciences Research Complex, University of St Andrews, BMS Building, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom.
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33
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Willemsen A, Carrasco JL, Elena SF, Zwart MP. Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses. Heredity (Edinb) 2018; 121:499-509. [PMID: 29743566 DOI: 10.1038/s41437-018-0086-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France
| | - José L Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, Spain.,The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Mark P Zwart
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands. .,Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
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McLeish MJ, Fraile A, García-Arenal F. Ecological Complexity in Plant Virus Host Range Evolution. Adv Virus Res 2018; 101:293-339. [PMID: 29908592 DOI: 10.1016/bs.aivir.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain.
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35
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Gómez‐Muñoz N, Velázquez K, Vives MC, Ruiz‐Ruiz S, Pina JA, Flores R, Moreno P, Guerri J. The resistance of sour orange to Citrus tristeza virus is mediated by both the salicylic acid and RNA silencing defence pathways. MOLECULAR PLANT PATHOLOGY 2017; 18:1253-1266. [PMID: 27588892 PMCID: PMC6638288 DOI: 10.1111/mpp.12488] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/26/2016] [Accepted: 08/30/2016] [Indexed: 05/08/2023]
Abstract
Citrus tristeza virus (CTV) induces in the field the decline and death of citrus varieties grafted on sour orange (SO) rootstock, which has forced the use of alternative decline-tolerant rootstocks in affected countries, despite the highly desirable agronomic features of the SO rootstock. Declining citrus plants display phloem necrosis below the bud union. In addition, SO is minimally susceptible to CTV compared with other citrus varieties, suggesting partial resistance of SO to CTV. Here, by silencing different citrus genes with a Citrus leaf blotch virus-based vector, we have examined the implication of the RNA silencing and salicylic acid (SA) defence pathways in the resistance of SO to CTV. Silencing of the genes RDR1, NPR1 and DCL2/DCL4, associated with these defence pathways, enhanced virus spread and accumulation in SO plants in comparison with non-silenced controls, whereas silencing of the genes NPR3/NPR4, associated with the hypersensitive response, produced a slight decrease in CTV accumulation and reduced stunting of SO grafted on CTV-infected rough lemon plants. We also found that the CTV RNA silencing suppressors p20 and p23 also suppress the SA signalling defence, with the suppressor activity being higher in the most virulent isolates.
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Affiliation(s)
- Neus Gómez‐Muñoz
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - Karelia Velázquez
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - María Carmen Vives
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - Susana Ruiz‐Ruiz
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - José Antonio Pina
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC), Universidad Politécnica de Valencia, Avenida de los NaranjosValencia46022Spain
| | - Pedro Moreno
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - José Guerri
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
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Kang SH, Atallah OO, Sun YD, Folimonova SY. Functional diversification upon leader protease domain duplication in the Citrus tristeza virus genome: Role of RNA sequences and the encoded proteins. Virology 2017; 514:192-202. [PMID: 29197719 DOI: 10.1016/j.virol.2017.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 01/14/2023]
Abstract
Viruses from the family Closteroviridae show an example of intra-genome duplications of more than one gene. In addition to the hallmark coat protein gene duplication, several members possess a tandem duplication of papain-like leader proteases. In this study, we demonstrate that domains encoding the L1 and L2 proteases in the Citrus tristeza virus genome underwent a significant functional divergence at the RNA and protein levels. We show that the L1 protease is crucial for viral accumulation and establishment of initial infection, whereas its coding region is vital for virus transport. On the other hand, the second protease is indispensable for virus infection of its natural citrus host, suggesting that L2 has evolved an important adaptive function that mediates virus interaction with the woody host.
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Affiliation(s)
- Sung-Hwan Kang
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
| | - Osama O Atallah
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
| | - Yong-Duo Sun
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
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Moury B, Fabre F, Hébrard E, Froissart R. Determinants of host species range in plant viruses. J Gen Virol 2017; 98:862-873. [PMID: 28475036 DOI: 10.1099/jgv.0.000742] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prediction of pathogen emergence is an important field of research, both in human health and in agronomy. Most studies of pathogen emergence have focused on the ecological or anthropic factors involved rather than on the role of intrinsic pathogen properties. The capacity of pathogens to infect a large set of host species, i.e. to possess a large host range breadth (HRB), is tightly linked to their emergence propensity. Using an extensive plant virus database, we found that four traits related to virus genome or transmission properties were strongly and robustly linked to virus HRB. Broader host ranges were observed for viruses with single-stranded genomes, those with three genome segments and nematode-transmitted viruses. Also, two contrasted groups of seed-transmitted viruses were evidenced. Those with a single-stranded genome had larger HRB than non-seed-transmitted viruses, whereas those with a double-stranded genome (almost exclusively RNA) had an extremely small HRB. From the plant side, the family taxonomic rank appeared as a critical threshold for virus host range, with a highly significant increase in barriers to infection between plant families. Accordingly, the plant-virus infectivity matrix shows a dual structure pattern: a modular pattern mainly due to viruses specialized to infect plants of a given family and a nested pattern due to generalist viruses. These results contribute to a better prediction of virus host jumps and emergence risks.
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Affiliation(s)
- Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | - Frédéric Fabre
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, F-33883 Villenave d'Ornon, France
| | - Eugénie Hébrard
- UMR186, IRD-Cirad-UM, Laboratory 'Interactions Plantes Microorganismes Environnement', Montpellier, France
| | - Rémy Froissart
- UMR5290, CNRS-IRD-UM1-UM2, Laboratory 'Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle', Montpellier, France.,UMR385, INRA-Cirad-SupAgro, Laboratory 'Biologie des Interactions Plantes-Parasites', Campus International de Baillarguet, F-34398 Montpellier, France
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38
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Kang SH, Dao TNM, Kim OK, Folimonova SY. Self-interaction of Citrus tristeza virus p33 protein via N-terminal helix. Virus Res 2017; 233:29-34. [PMID: 28279804 DOI: 10.1016/j.virusres.2017.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 11/28/2022]
Abstract
Citrus tristeza virus (CTV), the most economically important viral pathogen of citrus, encodes a unique protein, p33. CTV p33 shows no similarity with other known proteins, yet plays an important role in viral pathogenesis: it extends the virus host range and mediates virus ability to exclude superinfection by other variants of the virus. Previously we demonstrated that p33 is an integral membrane protein and appears to share characteristics of viral movement proteins. In this study, we show that the p33 protein self-interacts in vitro and in vivo using co-immunoprecipitation, yeast two hybrid, and bimolecular fluorescence complementation assays. Furthermore, a helix located at the N-terminus of the protein is required and sufficient for the protein self-interaction.
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Affiliation(s)
- Sung-Hwan Kang
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
| | - Thi Nguyet Minh Dao
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
| | - Ok-Kyung Kim
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
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Dalio RJD, Magalhães DM, Rodrigues CM, Arena GD, Oliveira TS, Souza-Neto RR, Picchi SC, Martins PMM, Santos PJC, Maximo HJ, Pacheco IS, De Souza AA, Machado MA. PAMPs, PRRs, effectors and R-genes associated with citrus-pathogen interactions. ANNALS OF BOTANY 2017; 119:749-774. [PMID: 28065920 PMCID: PMC5571375 DOI: 10.1093/aob/mcw238] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 07/08/2016] [Accepted: 10/22/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Recent application of molecular-based technologies has considerably advanced our understanding of complex processes in plant-pathogen interactions and their key components such as PAMPs, PRRs, effectors and R-genes. To develop novel control strategies for disease prevention in citrus, it is essential to expand and consolidate our knowledge of the molecular interaction of citrus plants with their pathogens. SCOPE This review provides an overview of our understanding of citrus plant immunity, focusing on the molecular mechanisms involved in the interactions with viruses, bacteria, fungi, oomycetes and vectors related to the following diseases: tristeza, psorosis, citrus variegated chlorosis, citrus canker, huanglongbing, brown spot, post-bloom, anthracnose, gummosis and citrus root rot.
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Affiliation(s)
- Ronaldo J. D. Dalio
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Diogo M. Magalhães
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Carolina M. Rodrigues
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Gabriella D. Arena
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Tiago S. Oliveira
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Reinaldo R. Souza-Neto
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Simone C. Picchi
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Paula M. M. Martins
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Paulo J. C. Santos
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Heros J. Maximo
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Inaiara S. Pacheco
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Alessandra A. De Souza
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Marcos A. Machado
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
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40
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Nummert G, Sõmera M, Uffert G, Abner E, Truve E. P1-independent replication and local movement of Rice yellow mottle virus in host and non-host plant species. Virology 2017; 502:28-32. [PMID: 27960111 DOI: 10.1016/j.virol.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/04/2016] [Accepted: 12/06/2016] [Indexed: 11/18/2022]
Abstract
Sobemovirus P1 protein, characterized previously as a suppressor of posttranscriptional gene silencing, is required for systemic virus spread and infection in plants. Mutations in the ORF1 initiation codon do not affect viral replication indicating P1 is not necessary for this process. Wild type, recombinant and P1 deletion mutants of Cocksfoot mottle virus and Rice yellow mottle virus were used to infect oat, rice, wheat, barley, Arabidopsis thaliana and Nicotiana benthamiana plants. Wild type RYMV, RYMV without P1 and RYMV with CfMV P1 were detected in inoculated leaves of all tested plant species. We found that RYMV does not need P1 for replication and for local movement neither in host nor non-host species tested in this study. However, it is crucial for successful systemic spread of the virus in its host plant rice. Moreover, adding CfMV P1 into RYMV genome did not help it to overcome restriction to the inoculated leaf.
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Affiliation(s)
- Grete Nummert
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Gabriela Uffert
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Erik Abner
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
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41
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Erokhina TN, Lazareva EA, Richert-Pöggeler KR, Sheval EV, Solovyev AG, Morozov SY. Subcellular Localization and Detection of Tobacco mosaic virus ORF6 Protein by Immunoelectron Microscopy. BIOCHEMISTRY. BIOKHIMIIA 2017; 82:60-66. [PMID: 28320287 DOI: 10.1134/s0006297917010060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated. In this study, using biochemical and immunological methods, we have shown that ORF6 peptide is accumulated after infection in case of two isolates of Tobacco mosaic virus strain U1 (TMV-U1 common and TMV-U1 isolate A15). Unlike virus particles accumulating in the cytoplasm, the product of the ORF6 gene is found mainly in nuclei, which correlates with previously published data about transient expression of ORF6 isolated from TMV-U1. Moreover, we present new data showing the presence of ORF6 genes in genomes of several tobamoviruses. For example, in the genomes of other members of the tobamovirus subgroup 1, including Rehmannia mosaic virus, Paprika mild mottle virus, Tobacco mild green mosaic virus, Tomato mosaic virus, Tomato mottle mosaic virus, and Nigerian tobacco latent virus, sequence comparisons revealed the existence of a similar open reading frame like ORF6 of TMV.
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Affiliation(s)
- T N Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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42
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Cook G, van Vuuren SP, Breytenbach JHJ, Steyn C, Burger JT, Maree HJ. Characterization of Citrus tristeza virus Single-Variant Sources in Grapefruit in Greenhouse and Field Trials. PLANT DISEASE 2016; 100:2251-2256. [PMID: 30682917 DOI: 10.1094/pdis-03-16-0391-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus tristeza virus (CTV) is endemic to southern Africa and the stem pitting syndrome that it causes was a limiting factor in grapefruit production prior to the introduction of cross-protection in the Citrus Improvement Scheme. This disease mitigation strategy, using various field-derived CTV sources, has significantly extended the productive lifespan of grapefruit orchards in South Africa. CTV commonly occurs as a population of various strains, masking the phenotypic effect of individual strains. Likewise, current South African CTV cross-protection sources are strain mixtures, obscuring an understanding of which strains are influencing cross-protection. The severity of various CTV strains has mostly been assessed on sensitive indicator hosts, but their effect on commercial varieties has seldom been investigated. Single-variant CTV isolates were used to investigate the phenotypic expression of CTV strains in commercial grapefruit varieties as well as CTV indicator hosts. They were biologically characterized for their ability to cause stem pitting and their rate of translocation and titer in the different hosts, monitored by enzyme-linked immunosorbent assay. Complete genome sequences for three CTV strain variants were generated. Isolates of CTV strains VT, T68, RB, and HA16-5 did not induce severe stem pitting in four grapefruit hosts in a glasshouse trial. Viral titers of the strains differed in the grapefruit hosts, but the RB isolate reached a higher titer in the grapefruit hosts compared with the VT, T68, and HA16-5 isolates. Additionally, horticultural assessment of two grapefruit varieties inoculated with the RB isolate in two field trials demonstrated that mild stem pitting did not negatively influence the horticultural performance of the grapefruit trees over an eight-year assessment period. 'Star Ruby' trees containing the CTV source GFMS35 showed less stem pitting than trees inoculated with the RB isolate, but had smaller canopy volumes and lower yields than trees containing the RB isolate. This suggests that the influence of CTV sources on tree performance is not limited to the effect of stem pitting.
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Affiliation(s)
- Glynnis Cook
- Citrus Research International, Nelspruit, 1200, South Africa
| | | | | | - Chanel Steyn
- Citrus Research International, Nelspruit, 1200, South Africa
| | - Johan T Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Hans J Maree
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, 7599, South Africa, and Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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43
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Leastro MO, Pallás V, Resende RO, Sánchez-Navarro JA. The functional analysis of distinct tospovirus movement proteins (NS M) reveals different capabilities in tubule formation, cell-to-cell and systemic virus movement among the tospovirus species. Virus Res 2016; 227:57-68. [PMID: 27697453 DOI: 10.1016/j.virusres.2016.09.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/22/2022]
Abstract
The lack of infectious tospovirus clones to address reverse genetic experiments has compromised the functional analysis of viral proteins. In the present study we have performed a functional analysis of the movement proteins (NSM) of four tospovirus species Bean necrotic mosaic virus (BeNMV), Chrysanthemum stem necrosis virus (CSNV), Tomato chlorotic spot virus (TCSV) and Tomato spotted wilt virus (TSWV), which differ biologically and molecularly, by using the Alfalfa mosaic virus (AMV) model system. All NSM proteins were competent to: i) support the cell-to-cell and systemic transport of AMV, ii) generate tubular structures on infected protoplast and iii) transport only virus particles. However, the NSM of BeNMV (one of the most phylogenetically distant species) was very inefficient to support the systemic transport. Deletion assays revealed that the C-terminal region of the BeNMV NSM, but not that of the CSNV, TCSV and TSWV NSM proteins, was dispensable for cell-to-cell transport, and that all the non-functional C-terminal NSM mutants were unable to generate tubular structures. Bimolecular fluorescence complementation analysis revealed that the C-terminus of the BeNMV NSM was not required for the interaction with the cognate nucleocapsid protein, showing a different protein organization when compared with other movement proteins of the '30K family'. Overall, our results revealed clearly differences in functional aspects among movement proteins from divergent tospovirus species that have a distinct biological behavior.
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Affiliation(s)
- Mikhail O Leastro
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, Brazil.
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain.
| | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, Brazil.
| | - Jesús A Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain.
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Syller J, Grupa A. Antagonistic within-host interactions between plant viruses: molecular basis and impact on viral and host fitness. MOLECULAR PLANT PATHOLOGY 2016; 17:769-82. [PMID: 26416204 PMCID: PMC6638324 DOI: 10.1111/mpp.12322] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Double infections of related or unrelated viruses frequently occur in single plants, the viral agents being inoculated into the host plant simultaneously (co-infection) or sequentially (super-infection). Plants attacked by viruses activate sophisticated defence pathways which operate at different levels, often at significant fitness costs, resulting in yield reduction in crop plants. The occurrence and severity of the negative effects depend on the type of within-host interaction between the infecting viruses. Unrelated viruses generally interact with each other in a synergistic manner, whereas interactions between related viruses are mostly antagonistic. These can incur substantial fitness costs to one or both of the competitors. A relatively well-known antagonistic interaction is cross-protection, also referred to as super-infection exclusion. This type of interaction occurs when a previous infection with one virus prevents or interferes with subsequent infection by a homologous second virus. The current knowledge on why and how one virus variant excludes or restricts another is scant. Super-infection exclusion between viruses has predominantly been attributed to the induction of RNA silencing, which is a major antiviral defence mechanism in plants. There are, however, presumptions that various mechanisms are involved in this phenomenon. This review outlines the current state of knowledge concerning the molecular mechanisms behind antagonistic interactions between plant viruses. Harmful or beneficial effects of these interactions on viral and host plant fitness are also characterized. Moreover, the review briefly outlines the past and present attempts to utilize antagonistic interactions among viruses to protect crop plants against destructive diseases.
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Affiliation(s)
- Jerzy Syller
- Plant Breeding and Acclimatization Institute-National Research Institute, Laboratory of Phytopathology, Centre Młochów, 05-831, Młochów, Poland
| | - Anna Grupa
- Plant Breeding and Acclimatization Institute-National Research Institute, Laboratory of Phytopathology, Centre Młochów, 05-831, Młochów, Poland
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45
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Atallah OO, Kang SH, El-Mohtar CA, Shilts T, Bergua M, Folimonova SY. A 5′-proximal region of the Citrus tristeza virus genome encoding two leader proteases is involved in virus superinfection exclusion. Virology 2016; 489:108-15. [DOI: 10.1016/j.virol.2015.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/11/2015] [Accepted: 12/14/2015] [Indexed: 01/08/2023]
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46
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The evolution of emaraviruses is becoming more complex: seven segments identified in the causal agent of Rose rosette disease. Virus Res 2015; 210:241-4. [DOI: 10.1016/j.virusres.2015.08.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/08/2015] [Accepted: 08/10/2015] [Indexed: 11/20/2022]
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47
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Benítez-Galeano MJ, Rubio L, Bertalmío A, Maeso D, Rivas F, Colina R. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage. Viruses 2015; 7:4152-68. [PMID: 26205407 PMCID: PMC4517143 DOI: 10.3390/v7072814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/04/2015] [Accepted: 07/17/2015] [Indexed: 11/16/2022] Open
Abstract
Citrus Tristeza Virus (CTV) is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23). Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36) in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD) and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1) the genetic diversity of Uruguayan CTV isolates circulating in the country and (2) the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program.
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Affiliation(s)
- María José Benítez-Galeano
- Laboratorio de Virología Molecular, Centro Universitario Regional Noroeste (CENUR Noroeste), Universidad de la Republica (UdelaR), Rivera 1350, 50000 Salto, Uruguay.
| | - Leticia Rubio
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Ana Bertalmío
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Diego Maeso
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Fernando Rivas
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Rodney Colina
- Laboratorio de Virología Molecular, Centro Universitario Regional Noroeste (CENUR Noroeste), Universidad de la Republica (UdelaR), Rivera 1350, 50000 Salto, Uruguay.
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48
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Soler N, Fagoaga C, López C, Moreno P, Navarro L, Flores R, Peña L. Symptoms induced by transgenic expression of p23 from Citrus tristeza virus in phloem-associated cells of Mexican lime mimic virus infection without the aberrations accompanying constitutive expression. MOLECULAR PLANT PATHOLOGY 2015; 16:388-99. [PMID: 25171669 PMCID: PMC6638416 DOI: 10.1111/mpp.12188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Citrus tristeza virus (CTV) is phloem restricted in natural citrus hosts. The 23-kDa protein (p23) encoded by the virus is an RNA silencing suppressor and a pathogenicity determinant. The expression of p23, or its N-terminal 157-amino-acid fragment comprising the zinc finger and flanking basic motifs, driven by the constitutive 35S promoter of cauliflower mosaic virus, induces CTV-like symptoms and other aberrations in transgenic citrus. To better define the role of p23 in CTV pathogenesis, we compared the phenotypes of Mexican lime transformed with p23-derived transgenes from the severe T36 and mild T317 CTV isolates under the control of the phloem-specific promoter from Commelina yellow mottle virus (CoYMV) or the 35S promoter. Expression of the constructs restricted to the phloem induced a phenotype resembling CTV-specific symptoms (vein clearing and necrosis, and stem pitting), but not the non-specific aberrations (such as mature leaf epinasty and yellow pinpoints, growth cessation and apical necrosis) observed when p23 was ectopically expressed. Furthermore, vein necrosis and stem pitting in Mexican lime appeared to be specifically associated with p23 from T36. Phloem-specific accumulation of the p23Δ158-209(T36) fragment was sufficient to induce the same anomalies, indicating that the region comprising the N-terminal 157 amino acids of p23 is responsible (at least in part) for the vein clearing, stem pitting and, possibly, vein corking in this host.
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Affiliation(s)
- Nuria Soler
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apdo. Oficial, Moncada, Valencia, 46113, Spain
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49
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Kang SH, Bak A, Kim OK, Folimonova SY. Membrane association of a nonconserved viral protein confers virus ability to extend its host range. Virology 2015; 482:208-17. [PMID: 25880112 DOI: 10.1016/j.virol.2015.03.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/17/2015] [Accepted: 03/20/2015] [Indexed: 12/16/2022]
Abstract
Citrus tristeza virus (CTV), the largest and most complex member of the family Closteroviridae, encodes a unique protein, p33, which shows no homology with other known proteins, however, plays an important role in virus pathogenesis. In this study, we examined some of the characteristics of p33. We show that p33 is a membrane-associated protein that is inserted into the membrane via a transmembrane helix formed by hydrophobic amino acid residues at the C-terminal end of the protein. Removal of this transmembrane domain (TMD) dramatically altered the intracellular localization of p33. Moreover, the TMD alone was sufficient to confer membrane localization of an unrelated protein. Finally, a CTV variant that produced a truncated p33 lacking the TMD was unable to infect sour orange, one of the selected virus hosts, which infection requires p33, suggesting that membrane association of p33 is important for the ability of CTV to extend its host range.
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Affiliation(s)
- Sung-Hwan Kang
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
| | - Aurélie Bak
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
| | - Ok-Kyung Kim
- University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA
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Dawson WO, Bar-Joseph M, Garnsey SM, Moreno P. Citrus tristeza virus: making an ally from an enemy. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:137-55. [PMID: 25973695 DOI: 10.1146/annurev-phyto-080614-120012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Virus diseases of perennial trees and vines have characteristics not amenable to study using small model annual plants. Unique disease symptoms such as graft incompatibilities and stem pitting cause considerable crop losses. Also, viruses in these long-living plants tend to accumulate complex populations of viruses and strains. Considerable progress has been made in understanding the biology and genetics of Citrus tristeza virus (CTV) and in developing it into a tool for crop protection and improvement. The diseases in tree and vine crops have commonalities for which CTV can be used to develop a baseline. The purpose of this review is to provide a necessary background of systems and reagents developed for CTV that can be used for continued progress in this area and to point out the value of the CTV-citrus system in answering important questions on plant-virus interactions and developing new methods for controlling plant diseases.
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Affiliation(s)
- William O Dawson
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, Florida 33850; ,
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