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Wang D, Chen M, Peng J, Zheng H, Lu Y, Wu G, Wu J, Li J, Chen J, Yan F, Rao S. Transcriptome Analysis of Tomato Leaves Reveals Candidate Genes Responsive to Tomato Brown Rugose Fruit Virus Infection. Int J Mol Sci 2024; 25:4012. [PMID: 38612822 PMCID: PMC11012278 DOI: 10.3390/ijms25074012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-22 genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
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Alcaide C, Donaire L, Aranda MA. Transcriptome analyses unveiled differential regulation of AGO and DCL genes by pepino mosaic virus strains. MOLECULAR PLANT PATHOLOGY 2022; 23:1592-1607. [PMID: 35852033 PMCID: PMC9562736 DOI: 10.1111/mpp.13249] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/21/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Pepino mosaic virus (PepMV) is a single-stranded (ss), positive-sense (+) RNA potexvirus that affects tomato crops worldwide. We have described an in planta antagonistic interaction between PepMV isolates of two strains in which the EU isolate represses the accumulation of the CH2 isolate during mixed infections. Reports describing transcriptomic responses to mixed infections are scant. We carried out transcriptomic analyses of tomato plants singly and mixed-infected with two PepMV isolates of both strains. Comparison of the transcriptomes of singly infected plants showed that deeper transcriptomic alterations occurred at early infection times, and also that each of the viral strains modulated the host transcriptome differentially. Mixed infections caused transcriptomic alterations similar to those for the sum of single infections at early infection times, but clearly differing at later times postinfection. We next tested the hypothesis that PepMV-EU, in either single or mixed infections, deregulates host gene expression differentially so that virus accumulation of both strains gets repressed. That seemed to be the case for the genes AGO1a, DCL2d, AGO2a, and DCL2b, which are involved in the antiviral silencing pathway and were upregulated by PepMV-EU but not by PepMV-CH2 at early times postinfection. The pattern of AGO2a expression was validated by reverse transcription-quantitative PCR in tomato and Nicotiana benthamiana plants. Using an N. benthamiana ago2 mutant line, we showed that AGO2 indeed plays an important role in the antiviral defence against PepMV, but it is not the primary determinant of the outcome of the antagonistic interaction between the two PepMV strains.
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Affiliation(s)
- Cristina Alcaide
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura‐CSICMurciaSpain
| | - Livia Donaire
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura‐CSICMurciaSpain
| | - Miguel A. Aranda
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura‐CSICMurciaSpain
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Xu XJ, Geng C, Jiang SY, Zhu Q, Yan ZY, Tian YP, Li XD. A maize triacylglycerol lipase inhibits sugarcane mosaic virus infection. PLANT PHYSIOLOGY 2022; 189:754-771. [PMID: 35294544 PMCID: PMC9157127 DOI: 10.1093/plphys/kiac126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 05/13/2023]
Abstract
Triacylglycerol lipase (TGL) plays critical roles in providing energy for seed germination and plant development. However, the role of TGL in regulating plant virus infection is largely unknown. In this study, we adopted affinity purification coupled with mass spectrometry and identified that a maize (Zea mays) pathogenesis-related lipase protein Z. mays TGL (ZmTGL) interacted with helper component-proteinase (HC-Pro) of sugarcane mosaic virus (SCMV). Yeast two-hybrid, luciferase complementation imaging, and bimolecular fluorescence complementation assays confirmed that ZmTGL directly interacted with SCMV HC-Pro in vitro and in vivo. The 101-460 residues of SCMV HC-Pro were important for its interaction with ZmTGL. ZmTGL and SCMV HC-Pro co-localized at the mitochondria. Silencing of ZmTGL facilitated SCMV infection, and over-expression of ZmTGL reduced the RNA silencing suppression activity, most likely through reducing HC-Pro accumulation. Our results provided evidence that the lipase hydrolase activity of ZmTGL was associated with reducing HC-Pro accumulation, activation of salicylic acid (SA)-mediated defense response, and inhibition of SCMV infection. We show that ZmTGL inhibits SCMV infection by reducing HC-Pro accumulation and activating the SA pathway.
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Affiliation(s)
- Xiao-Jie Xu
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chao Geng
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Shao-Yan Jiang
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Qing Zhu
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Author for correspondence:
| | - Xiang-Dong Li
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
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Zhou T, Zhou S, Chen Y, Wang J, Zhang R, Xiang H, Xia Z, An M, Zhao X, Wu Y. Next-generation sequencing identification and multiplex RT-PCR detection for viruses infecting cigar and flue-cured tobacco. Mol Biol Rep 2022; 49:237-247. [PMID: 34705219 DOI: 10.1007/s11033-021-06864-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Early, precise and simultaneous identification of plant viruses is of great significance for preventing virus spread and reducing losses in agricultural yields. METHODS AND RESULTS In this study, the identification of plant viruses from symptomatic samples collected from a cigar tobacco planting area in Deyang and a flue-cured tobacco planting area in Luzhou city, Sichuan Province, China, was conducted by deep sequencing of small RNAs (sRNAs) through an Illumina sequencing platform, and plant virus-specific contigs were generated based on virus-derived siRNA sequences. Additionally, sequence alignment and phylogenetic analysis were performed to determine the species or strains of these viruses. A total of 27930450, 21537662 and 28194021 clean reads were generated from three pooled samples, with a total of 105 contigs mapped to the closest plant viruses with lengths ranging from 34 ~ 1720 nt. The results indicated that the major viruses were potato virus Y, Chilli veinal mottle virus, tobacco vein banding mosaic virus, tobacco mosaic virus and cucumber mosaic virus. Subsequently, a fast and sensitive multiplex reverse transcription polymerase chain reaction assay was developed for the simultaneous detection of the most frequent RNA viruses infecting cigar and flue-cured tobacco in Sichuan. CONCLUSIONS These results provide a theoretical basis and convenient methods for the rapid detection and control of viruses in cigar- and flue-cured tobacco.
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Affiliation(s)
- Tao Zhou
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Shidong Zhou
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Yong Chen
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Jun Wang
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Ruina Zhang
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Huan Xiang
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Xiuxiang Zhao
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China.
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China.
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Martin IR, Vigne E, Velt A, Hily JM, Garcia S, Baltenweck R, Komar V, Rustenholz C, Hugueney P, Lemaire O, Schmitt-Keichinger C. Severe Stunting Symptoms upon Nepovirus Infection Are Reminiscent of a Chronic Hypersensitive-like Response in a Perennial Woody Fruit Crop. Viruses 2021; 13:2138. [PMID: 34834945 PMCID: PMC8625034 DOI: 10.3390/v13112138] [Citation(s) in RCA: 9] [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: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/02/2022] Open
Abstract
Virus infection of plants can result in various degrees of detrimental impacts and disparate symptom types and severities. Although great strides have been made in our understanding of the virus-host interactions in herbaceous model plants, the mechanisms underlying symptom development are poorly understood in perennial fruit crops. Grapevine fanleaf virus (GFLV) causes variable symptoms in most vineyards worldwide. To better understand GFLV-grapevine interactions in relation to symptom development, field and greenhouse trials were conducted with a grapevine genotype that exhibits distinct symptoms in response to a severe and a mild strain of GFLV. After validation of the infection status of the experimental vines by high-throughput sequencing, the transcriptomic and metabolomic profiles in plants infected with the two viral strains were tested and compared by RNA-Seq and LC-MS, respectively, in the differentiating grapevine genotype. In vines infected with the severe GFLV strain, 1023 genes, among which some are implicated in the regulation of the hypersensitive-type response, were specifically deregulated, and a higher accumulation of resveratrol and phytohormones was observed. Interestingly, some experimental vines restricted the virus to the rootstock and remained symptomless. Our results suggest that GFLV induces a strain- and cultivar-specific defense reaction similar to a hypersensitive reaction. This type of defense leads to a severe stunting phenotype in some grapevines, whereas others are resistant. This work is the first evidence of a hypersensitive-like reaction in grapevine during virus infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Corinne Schmitt-Keichinger
- Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, 68000 Colmar, France; (E.V.); (A.V.); (J.-M.H.); (S.G.); (R.B.); (V.K.); (C.R.); (P.H.); (O.L.)
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Cheng DJ, Xu XJ, Yan ZY, Tettey CK, Fang L, Yang GL, Geng C, Tian YP, Li XD. The chloroplast ribosomal protein large subunit 1 interacts with viral polymerase and promotes virus infection. PLANT PHYSIOLOGY 2021; 187:174-186. [PMID: 34618134 PMCID: PMC8418413 DOI: 10.1093/plphys/kiab249] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 05/18/2023]
Abstract
Chloroplasts play an indispensable role in the arms race between plant viruses and hosts. Chloroplast proteins are often recruited by plant viruses to support viral replication and movement. However, the mechanism by which chloroplast proteins regulate potyvirus infection remains largely unknown. In this study, we observed that Nicotiana benthamiana ribosomal protein large subunit 1 (NbRPL1), a chloroplast ribosomal protein, localized to the chloroplasts via its N-terminal 61 amino acids (transit peptide), and interacted with tobacco vein banding mosaic virus (TVBMV) nuclear inclusion protein b (NIb), an RNA-dependent RNA polymerase. Upon TVBMV infection, NbRPL1 was recruited into the 6K2-induced viral replication complexes in chloroplasts. Silencing of NbRPL1 expression reduced TVBMV replication. NbRPL1 competed with NbBeclin1 to bind NIb, and reduced the NbBeclin1-mediated degradation of NIb. Therefore, our results suggest that NbRPL1 interacts with NIb in the chloroplasts, reduces NbBeclin1-mediated NIb degradation, and enhances TVBMV infection.
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Affiliation(s)
- De-Jie Cheng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiao-Jie Xu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Carlos Kwesi Tettey
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Le Fang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Guang-Ling Yang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chao Geng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiang-Dong Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
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Zhao CY, Xue HW. PI4Kγ2 Interacts with E3 Ligase MIEL1 to Regulate Auxin Metabolism and Root Development. PLANT PHYSIOLOGY 2020; 184:933-944. [PMID: 32788299 PMCID: PMC7536656 DOI: 10.1104/pp.20.00799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/20/2020] [Indexed: 05/07/2023]
Abstract
Root development is important for normal plant growth and nutrient absorption. Studies have revealed the involvement of various factors in this complex process, improving our understanding of the relevant regulatory mechanisms. Here, we functionally characterize the role of Arabidopsis (Arabidopsis thaliana) phosphatidylinositol 4-kinase γ2 (PI4Kγ2) in root elongation regulation, which functions to modulate stability of the RING-type E3 ligase MYB30-INTERACTING E3 LIGASE1 (MIEL1) and auxin metabolism. Mutant plants deficient in PI4Kγ2 (pi4kγ2) exhibited a shortened root length and elongation zone due to reduced auxin level. PI4Kγ2 was shown to interact with MIEL1, regulating its degradation and furthering the stability of transcription factor MYB30 (which suppresses auxin metabolism by directly binding to promoter regions of GH3 2 and GH3 6). Interestingly, pi4kγ2 plants presented altered hypersensitive response, indicating that PI4Kγ2 regulates synergetic growth and defense of plants through modulating auxin metabolism. These results reveal the importance of protein interaction in regulating ubiquitin-mediated protein degradation in eukaryotic cells, and illustrate a mechanism coordinating plant growth and biotic stress response.
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Affiliation(s)
- Chun-Yan Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Wei Xue
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Xu XJ, Li HG, Cheng DJ, Liu LZ, Geng C, Tian YP, Li XD. A Spontaneous Complementary Mutation Restores the RNA Silencing Suppression Activity of HC-Pro and the Virulence of Sugarcane Mosaic Virus. FRONTIERS IN PLANT SCIENCE 2020; 11:1279. [PMID: 32973838 PMCID: PMC7472499 DOI: 10.3389/fpls.2020.01279] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/05/2020] [Indexed: 05/26/2023]
Abstract
Cross-protection is a promising measure to control plant viral diseases. Reverse genetics had been recently adopted to generate attenuated mutants that have potential in cross-protection. But studies on the variability of the progeny viruses of the attenuated mutants are scarce. Sugarcane mosaic virus (SCMV; genus Potyvirus, family Potyviridae) is the prevalent virus inducing maize dwarf mosaic disease in China. Here, we showed that the substitution of arginine with isoleucine in the FRNK motif at position 184 of helper component-proteinase (HC-Pro) abolished its RNA silencing suppression (RSS) activity, drastically reduced the virulence and accumulation level of SCMV, and impaired the synergism between SCMV and maize chlorotic mottle virus. The attenuated mutant could protect maize plants from a severe infection of SCMV. However, a spontaneous mutation of glycine at position 440 to arginine in HC-Pro rescued the virulence and synergism with maize chlorotic mottle virus of SCMV and the RSS activity of HC-Pro. Similar results were obtained with tobacco vein banding mosaic virus and watermelon mosaic virus. These results provide novel evidence for the complementary mutation of potyviruses in maintaining the HC-Pro RSS activity and potyviral virulence and remind us of evaluating the potential risk of attenuated mutants thoroughly before applying for the control of plant viral diseases via cross-protection.
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Affiliation(s)
- Xiao-Jie Xu
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Huan-Gai Li
- Protein Science Laboratory of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - De-Jie Cheng
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Ling-Zhi Liu
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Chao Geng
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan-Ping Tian
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Xiang-Dong Li
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
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Xu M, Chen J, Huang Y, Shen D, Sun P, Xu Y, Tao X. Dynamic Transcriptional Profiles of Arabidopsis thaliana Infected by Tomato spotted wilt virus. PHYTOPATHOLOGY 2020; 110:153-163. [PMID: 31544594 DOI: 10.1094/phyto-06-19-0199-fi] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tomato spotted wilt virus (TSWV) is a negative-stranded RNA virus that infects hundreds of plant species, causing great economic loss. Infected Arabidopsis thaliana plants develop symptoms including chlorosis and wilt, which can lead to cell death. From 9 to 15 days after TSWV infection, symptoms progress through a three-stage process of appearance, severity, and death. In this study, deep sequencing technology was first used to explore gene expression in response to TSWV infection in model plant A. thaliana at different symptom development stages. We found that plant immune defense and protein degradation are induced by TSWV infection and that both inductions became stronger over time. The photosynthesis pathway was attenuated with TSWV infection. Cell wall metabolism had a large extent of downregulation while some genes were upregulated. These results illustrate the dynamic nature of TSWV infection in A. thaliana at the whole-transcriptome level. The link between biological processes and subpathway metabolism was further analyzed. Our study provides new insight into host regulatory networks and dynamic processes in response to TSWV infection.
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Affiliation(s)
- Min Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Jing Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Ying Huang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Peng Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yi Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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10
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Paudel DB, Sanfaçon H. Exploring the Diversity of Mechanisms Associated With Plant Tolerance to Virus Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:1575. [PMID: 30450108 PMCID: PMC6224807 DOI: 10.3389/fpls.2018.01575] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/09/2018] [Indexed: 05/17/2023]
Abstract
Tolerance is defined as an interaction in which viruses accumulate to some degree without causing significant loss of vigor or fitness to their hosts. Tolerance can be described as a stable equilibrium between the virus and its host, an interaction in which each partner not only accommodate trade-offs for survival but also receive some benefits (e.g., protection of the plant against super-infection by virulent viruses; virus invasion of meristem tissues allowing vertical transmission). This equilibrium, which would be associated with little selective pressure for the emergence of severe viral strains, is common in wild ecosystems and has important implications for the management of viral diseases in the field. Plant viruses are obligatory intracellular parasites that divert the host cellular machinery to complete their infection cycle. Highjacking/modification of plant factors can affect plant vigor and fitness. In addition, the toxic effects of viral proteins and the deployment of plant defense responses contribute to the induction of symptoms ranging in severity from tissue discoloration to malformation or tissue necrosis. The impact of viral infection is also influenced by the virulence of the specific virus strain (or strains for mixed infections), the host genotype and environmental conditions. Although plant resistance mechanisms that restrict virus accumulation or movement have received much attention, molecular mechanisms associated with tolerance are less well-understood. We review the experimental evidence that supports the concept that tolerance can be achieved by reaching the proper balance between plant defense responses and virus counter-defenses. We also discuss plant translation repression mechanisms, plant protein degradation or modification pathways and viral self-attenuation strategies that regulate the accumulation or activity of viral proteins to mitigate their impact on the host. Finally, we discuss current progress and future opportunities toward the application of various tolerance mechanisms in the field.
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Affiliation(s)
- Dinesh Babu Paudel
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
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11
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Hou H, Hu Y, Wang Q, Xu X, Qian Y, Zhou X. Gene Expression Profiling Shows That NbFDN1 Is Involved in Modulating the Hypersensitive Response-Like Cell Death Induced by the Oat dwarf virus RepA Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1006-1020. [PMID: 29649964 DOI: 10.1094/mpmi-12-17-0291-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we used high-throughput deep nucleotide sequencing to characterize the global transcriptional response of Nicotiana benthamiana plants to transient expression of the RepA protein from Oat dwarf virus (ODV). We identified 7,878 significantly differentially expressed genes (DEG) that mapped to 125 pathways, suggesting that comprehensive networks are involved in regulation of RepA-induced cell death. Of the 202 DEG associated with photosynthesis, expression of 195 was found to be downregulated, indicating a significant inhibition of photosynthesis in response to RepA expression, which is associated with chloroplast disruption and physiological changes. We focused our analysis on NbFDN1, a member of the ferredoxin protein family that participates in the chloroplast electron transport chain performing oxygenic photosynthesis, which was identified to directly interact with NbTsip1. We separately knocked down the expression of NbFDN1 and NbTsip1 using virus-induced gene silencing, and found that NbFDN1 silencing speeded up the development of RepA-induced cell death, unlike NbTsip1 silencing, which showed an opposite effect on RepA-induced response. Further study showed increased H2O2 accumulation and a negative correlation between the transcripts of NbFDN1 and NbTsip1 in NbFDN1-silenced plants. Hence, we speculate that NbFDN1 has an effect on RepA-induced hypersensitive response-like response by modulating NbTsip1 transcription as well as H2O2 production.
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Affiliation(s)
- Huwei Hou
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Ya Hu
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Qian Wang
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Xiongbiao Xu
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Yajuan Qian
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Xueping Zhou
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
- 2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
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Cervera H, Ambrós S, Bernet GP, Rodrigo G, Elena SF. Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study. Mol Biol Evol 2018; 35:1599-1615. [PMID: 29562354 PMCID: PMC5995217 DOI: 10.1093/molbev/msy038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts.
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Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Silvia Ambrós
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Guillermo P Bernet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, Paterna, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, NM
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13
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Huang C, Cun Y, Yu H, Tong Z, Xiao B, Song Z, Wang B, Li Y, Liu Y. Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infection. Virol J 2017; 14:153. [PMID: 28807054 PMCID: PMC5557316 DOI: 10.1186/s12985-017-0821-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/07/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Tomato zonate spot virus (TZSV), a dominant species of thrips-transmitted orthotospoviruses in Yunnan and Guangxi provinces in China, causes significant loss of yield in lots of crops and is a major threat to incomes of rural families. However, the detailed molecular mechanism of crop disease caused by TZSV remains obscure. METHODS Next-generation sequencing (NGS)-based transcriptome analysis (RNA-seq) was performed to investigate and compare the gene expression changes in systemic leaves of tobacco upon infection with TZSV and mock-inoculated plants as a control. RESULTS De novo assembly and analysis of tobacco transcriptome data by RNA-Seq identified 135,395 unigenes. 2102 differentially expressed genes (DEGs) were obtained in tobacco with TZSV infection, among which 1518 DEGs were induced and 584 were repressed. Gene Ontology enrichment analysis revealed that these DEGs were associated with multiple biological functions, including metabolic process, oxidation-reduction process, photosynthesis process, protein kinase activity. The KEGG pathway analysis of these DEGs indicated that pathogenesis caused by TZSV may affect multiple processes including primary and secondary metabolism, photosynthesis and plant-pathogen interactions. CONCLUSION Our global survey of transcriptional changes in TZSV infected tobacco provides crucial information into the precise molecular mechanisms underlying pathogenesis and symptom development. This is the first report on the relationships in the TZSV-plant interaction using transcriptome analysis. Findings of present study will significantly help enhance our understanding of the complicated mechanisms of plant responses to orthotospoviral infection.
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Affiliation(s)
- Changjun Huang
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Yupeng Cun
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Haiqin Yu
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Zhijun Tong
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Bingguang Xiao
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Zhongbang Song
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Bingwu Wang
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Yongping Li
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
| | - Yong Liu
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming, 650021 China
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Geng C, Yan ZY, Cheng DJ, Liu J, Tian YP, Zhu CX, Wang HY, Li XD. Tobacco vein banding mosaic virus 6K2 Protein Hijacks NbPsbO1 for Virus Replication. Sci Rep 2017; 7:43455. [PMID: 28230184 PMCID: PMC5322494 DOI: 10.1038/srep43455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/23/2017] [Indexed: 01/18/2023] Open
Abstract
Chloroplast-bound vesicles are key components in viral replication complexes (VRCs) of potyviruses. The potyviral VRCs are induced by the second 6 kDa protein (6K2) and contain at least viral RNA and nuclear inclusion protein b. To date, no chloroplast protein has been identified to interact with 6K2 and involve in potyvirus replication. In this paper, we showed that the Photosystem II oxygen evolution complex protein of Nicotiana benthamiana (NbPsbO1) was a chloroplast protein interacting with 6K2 of Tobacco vein banding mosaic virus (TVBMV; genus Potyvirus) and present in the VRCs. The first 6 kDa protein (6K1) was recruited to VRCs by 6K2 but had no interaction with NbPSbO1. Knockdown of NbPsbO1 gene expression in N. benthamiana plants through virus-induced gene silencing significantly decreased the accumulation levels of TVBMV and another potyvirus Potato virus Y, but not Potato virus X of genus Potexvirus. Amino acid substitutions in 6K2 that disrupted its interaction with NbPsbO1 also affected the replication of TVBMV. NbPsbP1 and NbPsbQ1, two other components of the Photosystem II oxygen evolution complex had no interaction with 6K2 and no effect on TVBMV replication. To conclude, 6K2 recruits 6K1 to VRCs and hijacks chloroplast protein NbPsbO1 to regulate potyvirus replication.
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Affiliation(s)
- Chao Geng
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - De-Jie Cheng
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Jin Liu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chang-Xiang Zhu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Shandong Provincial Key laboratory for Agricultural Microbiology, Tai’an, Shandong, 271018, China
| | - Hong-Yan Wang
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiang-Dong Li
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Shandong Provincial Key laboratory for Agricultural Microbiology, Tai’an, Shandong, 271018, China
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