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Zhao Z, Zhu Z, Jiao Y, Zhang G. Pan-genome analysis of GT64 gene family and expression response to Verticillium wilt in cotton. BMC PLANT BIOLOGY 2024; 24:893. [PMID: 39343881 PMCID: PMC11440917 DOI: 10.1186/s12870-024-05584-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND The GT64 subfamily, belonging to the glycosyltransferase family, plays a critical function in plant adaptation to stress conditions and the modulation of plant growth, development, and organogenesis processes. However, a comprehensive identification and systematic analysis of GT64 in cotton are still lacking. RESULTS This study used bioinformatics techniques to conduct a detailed investigation on the GT64 gene family members of eight cotton species for the first time. A total of 39 GT64 genes were detected, which could be classified into five subfamilies according to the phylogenetic tree. Among them, six genes were found in upland cotton. Furthermore, investigated the precise chromosomal positions of these genes and visually represented their gene structure details. Moreover, forecasted cis-regulatory elements in GhGT64s and ascertained the duplication type of the GT64 in the eight cotton species. Evaluation of the Ka/Ks ratio for similar gene pairs among the eight cotton species provided insights into the selective pressures acting on these homologous genes. Additionally, analyzed the expression profiles of the GT64 gene family. Overexpressing GhGT64_4 in tobacco improved its disease resistance. Subsequently, VIGS experiments conducted in cotton demonstrated reduced disease resistance upon silencing of the GhGT64_4, may indicate its involvement in affecting lignin and jasmonic acid biosynthesis pathways, thus impacting cotton resistance. Weighted Gene Co-expression Network Analysis (WGCNA) revealed an early immune response against Verticillium dahliae in G. barbadense compared to G. hirsutum. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis indicated that some GT64 genes might play a role under various biotic and abiotic stress conditions. CONCLUSIONS These discoveries enhance our knowledge of GT64 family members and lay the groundwork for future investigations into the disease resistance mechanisms of this gene in cotton.
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Affiliation(s)
- Zengqiang Zhao
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi, Xinjiang, 832000, China
| | - Zongcai Zhu
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi, Xinjiang, 832000, China
| | - Yang Jiao
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, China.
| | - Guoli Zhang
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi, Xinjiang, 832000, China.
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2
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Hong Y, Wei R, Li C, Cai H, Chen E, Pan X, Zhang W. Establishment of virus-induced gene-silencing system in Juglans sigillata Dode and functional analysis of JsFLS2 and JsFLS4. Gene 2024; 913:148385. [PMID: 38493973 DOI: 10.1016/j.gene.2024.148385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Juglans sigillata Dode is one of the important tree species in southwest China, and it has significant economic and ecological value. However, there is still a lack of effective methods to identify the functional genes of J. sigillata. By verifying the model plant tobacco, the pTRV2::JsPDS vector was able to cause photobleaching. This study showed that photobleaching occurred 24 and 30 d after the silencing vector was infected with aseptic seedlings and fruits of J. sigillata, respectively. When the OD600 was 0.6, and the injection dose was 500 μL, the gene silencing efficiency of aseptic seedlings was the highest at 16.7 %, significantly better than other treatments. Moreover, when the OD600 was 0.8, and the injection dose was 500 μL, the gene silencing efficiency in the walnut fruit was the highest (20 %). In addition, the VIGS system was successfully used to silence JsFLS2 and JsFLS4 genes in J. sigillata. This study also showed that the flavonol content and gene expression in the treatment group were decreased compared to the control group. In addition, the proteins transcribed and translated from the JsFLS4 gene may have higher catalytic activity for dihydroquercetin. The above results indicate that the TRV-mediated VIGS system can be an ideal tool for studying J. sigillata gene function.
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Affiliation(s)
- Yanyang Hong
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Rong Wei
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Chunxiang Li
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Hu Cai
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Erjuan Chen
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Xuejun Pan
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China.
| | - Wen'e Zhang
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China.
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3
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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4
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Zhang G, Jiao Y, Zhao Z, Chen Q, Wang Z, Zhu J, Lv N, Sun G. Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum. Genes (Basel) 2024; 15:348. [PMID: 38540407 PMCID: PMC10970331 DOI: 10.3390/genes15030348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 06/14/2024] Open
Abstract
Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.
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Affiliation(s)
- Guoli Zhang
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi 832000, China; (G.Z.)
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Y.J.)
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shehezi 832000, China
| | - Yang Jiao
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Y.J.)
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shehezi 832000, China
- Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi 832000, China
| | - Zengqiang Zhao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shehezi 832000, China
- Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi 832000, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Y.J.)
| | - Zhijun Wang
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi 832000, China; (G.Z.)
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shehezi 832000, China
| | - Jincheng Zhu
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi 832000, China; (G.Z.)
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shehezi 832000, China
| | - Ning Lv
- Xinjiang Academy of Agricultural and Reclamation, 221 Wuyi Highway, Shihezi 832000, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Liu Y, Lyu R, Singleton JJ, Patra B, Pattanaik S, Yuan L. A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants. PLANT METHODS 2024; 20:26. [PMID: 38347628 PMCID: PMC10860238 DOI: 10.1186/s13007-024-01154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) is widely used in plant functional genomics. However, the efficiency of VIGS in young plantlets varies across plant species. Additionally, VIGS is not optimized for many plant species, especially medicinal plants that produce valuable specialized metabolites. RESULTS We evaluated the efficacy of five-day-old, etiolated seedlings of Catharanthus roseus (periwinkle) for VIGS. The seedlings were vacuum-infiltrated with Agrobacterium tumefaciens GV3101 cells carrying the tobacco rattle virus (TRV) vectors. The protoporphyrin IX magnesium chelatase subunit H (ChlH) gene, a key gene in chlorophyll biosynthesis, was used as the target for VIGS, and we observed yellow cotyledons 6 days after infiltration. As expected, the expression of CrChlH and the chlorophyll contents of the cotyledons were significantly decreased after VIGS. To validate the cotyledon based-VIGS method, we silenced the genes encoding several transcriptional regulators of the terpenoid indole alkaloid (TIA) biosynthesis in C. roseus, including two activators (CrGATA1 and CrMYC2) and two repressors (CrGBF1 and CrGBF2). Silencing CrGATA1 led to downregulation of the vindoline pathway genes (T3O, T3R, and DAT) and decreased vindoline contents in cotyledons. Silencing CrMYC2, followed by elicitation with methyl jasmonate (MeJA), resulted in the downregulation of ORCA2 and ORCA3. We also co-infiltrated C. roseus seedlings with TRV vectors that silence both CrGBF1 and CrGBF2 and overexpress CrMYC2, aiming to simultaneous silencing two repressors while overexpressing an activator. The simultaneous manipulation of repressors and activator resulted in significant upregulation of the TIA pathway genes. To demonstrate the broad application of the cotyledon-based VIGS method, we optimized the method for two other valuable medicinal plants, Glycyrrhiza inflata (licorice) and Artemisia annua (sweet wormwood). When TRV vectors carrying the fragments of the ChlH genes were infiltrated into the seedlings of these plants, we observed yellow cotyledons with decreased chlorophyll contents. CONCLUSIONS The widely applicable cotyledon-based VIGS method is faster, more efficient, and easily accessible to additional treatments than the traditional VIGS method. It can be combined with transient gene overexpression to achieve simultaneous up- and down-regulation of desired genes in non-model plants. This method provides a powerful tool for functional genomics of medicinal plants, facilitating the discovery and production of valuable therapeutic compounds.
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Affiliation(s)
- Yongliang Liu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Ruiqing Lyu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Joshua J Singleton
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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6
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Yang W, Chen X, Chen J, Zheng P, Liu S, Tan X, Sun B. Virus-Induced Gene Silencing in the Tea Plant ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:3162. [PMID: 37687408 PMCID: PMC10490191 DOI: 10.3390/plants12173162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
The recent availability of a number of tea plant genomes has sparked substantial interest in using reverse genetics to explore gene function in tea (Camellia sinensis). However, a hurdle to this is the absence of an efficient transformation system, and virus-induced gene silencing (VIGS), a transient transformation system, could be an optimal choice for validating gene function in the tea plant. In this study, phytoene desaturase (PDS), a carotenoid biosynthesis gene, was used as a reporter to evaluate the VIGS system. The injection sites of the leaves (leaf back, petiole, and stem) for infiltration were tested, and the results showed that petiole injection had the most effective injection, without leading to necrotic lesions that cause the leaves to drop. Tea leaves were inoculated with Agrobacterium harboring a tobacco rattle virus plasmid (pTRV2) containing a CsPDS silencing fragment. The tea leaves exhibited chlorosis symptoms 7-14 days after inoculation, depending on the cultivar. In the chlorosis plants, the coat protein (CP) of tobacco rattle virus (TRV) was detected and coincided with the lower transcription of CsPDS and reduced chlorophyll content compared with the empty vector control, with 81.82% and 54.55% silencing efficiency of 'LTDC' and 'YSX', respectively. These results indicate that the VIGS system with petiole injection could quickly and effectively silence a gene in tea plants.
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Affiliation(s)
| | | | | | | | | | - Xindong Tan
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.Y.); (X.C.); (J.C.); (P.Z.); (S.L.)
| | - Binmei Sun
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.Y.); (X.C.); (J.C.); (P.Z.); (S.L.)
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7
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Qin L, Nong J, Cui K, Tang X, Gong X, Xia Y, Xu Y, Qiu Y, Li X, Xia S. SsCak1 Regulates Growth and Pathogenicity in Sclerotinia sclerotiorum. Int J Mol Sci 2023; 24:12610. [PMID: 37628791 PMCID: PMC10454577 DOI: 10.3390/ijms241612610] [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: 07/19/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Sclerotinia sclerotiorum is a devastating fungal pathogen that causes severe crop losses worldwide. It is of vital importance to understand its pathogenic mechanism for disease control. Through a forward genetic screen combined with next-generation sequencing, a putative protein kinase, SsCak1, was found to be involved in the growth and pathogenicity of S. sclerotiorum. Knockout and complementation experiments confirmed that deletions in SsCak1 caused defects in mycelium and sclerotia development, as well as appressoria formation and host penetration, leading to complete loss of virulence. These findings suggest that SsCak1 is essential for the growth, development, and pathogenicity of S. sclerotiorum. Therefore, SsCak1 could serve as a potential target for the control of S. sclerotiorum infection through host-induced gene silencing (HIGS), which could increase crop resistance to the pathogen.
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Affiliation(s)
- Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Jieying Nong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Kan Cui
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Xin Gong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Yunong Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Yan Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yilan Qiu
- Department of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
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8
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Newman TE, Kim H, Khentry Y, Sohn KH, Derbyshire MC, Kamphuis LG. The broad host range pathogen Sclerotinia sclerotiorum produces multiple effector proteins that induce host cell death intracellularly. MOLECULAR PLANT PATHOLOGY 2023; 24:866-881. [PMID: 37038612 PMCID: PMC10346375 DOI: 10.1111/mpp.13333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Sclerotinia sclerotiorum is a broad host range necrotrophic fungal pathogen, which causes disease on many economically important crop species. S. sclerotiorum has been shown to secrete small effector proteins to kill host cells and acquire nutrients. We set out to discover novel necrosis-inducing effectors and characterize their activity using transient expression in Nicotiana benthamiana leaves. Five intracellular necrosis-inducing effectors were identified with differing host subcellular localization patterns, which were named intracellular necrosis-inducing effector 1-5 (SsINE1-5). We show for the first time a broad host range pathogen effector, SsINE1, that uses an RxLR-like motif to enter host cells. Furthermore, we provide preliminary evidence that SsINE5 induces necrosis via an NLR protein. All five of the identified effectors are highly conserved in globally sourced S. sclerotiorum isolates. Taken together, these results advance our understanding of the virulence mechanisms employed by S. sclerotiorum and reveal potential avenues for enhancing genetic resistance to this damaging fungal pathogen.
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Affiliation(s)
- Toby E. Newman
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Haseong Kim
- Plant Immunity Research CenterSeoul National UniversitySeoul08826Republic of Korea
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kee Hoon Sohn
- Plant Immunity Research CenterSeoul National UniversitySeoul08826Republic of Korea
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Republic of Korea
- Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Mark C. Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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9
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Cheng G, Shu X, Wang Z, Wang N, Zhang F. Establishing a Virus-Induced Gene Silencing System in Lycoris chinensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:2458. [PMID: 37447019 DOI: 10.3390/plants12132458] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023]
Abstract
Lycoris is an important plant with both medicinal and ornamental values. However, it does not have an efficient genetic transformation system, which makes it difficult to study gene function of the genus. Virus-induced gene silencing (VIGS) is an effective technique for studying gene functions in plants. In this study, we develop an efficient virus-induced gene-silencing (VIGS) system using the leaf tip needle injection method. The widely used TRV vector is constructed, and the Cloroplastos Alterados 1 (CLA1) and Phytoene Desaturase (PDS) genes are selected as visual indicators in the VIGS system. As a result, it is observed that leaves infected with TRV-LcCLA1 and TRV-LcPDS both show a yellowing phenotype (loss of green), and the chlorosis range of TRV-LcCLA1 was larger and deeper than that of TRV-LcPDS. qRT-PCR results show that the expression levels of LcCLA1 and LcPDS are significantly reduced, and the silencing efficiency of LcCLA1 is higher than that of LcPDS. These results indicate that the VIGS system of L. chinensis was preliminarily established, and LcCLA1 is more suitable as a gene-silencing indicator. For the monocotyledonous plant leaves with a waxy surface, the leaf tip injection method greatly improves the infiltration efficiency. The newly established VIGS system will contribute to gene functional research in Lycoris species.
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Affiliation(s)
- Guanghao Cheng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
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10
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Chang YL, Huang LM, Kuo XZ, Chen YY, Lin ST, Jeng MF, Yeh HH, Tsai WC, Chen HH. PbABCG1 and PbABCG2 transporters are required for the emission of floral monoterpenes in Phalaenopsis bellina. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:279-292. [PMID: 36738107 DOI: 10.1111/tpj.16133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 12/17/2022] [Accepted: 01/30/2023] [Indexed: 05/10/2023]
Abstract
Terrestrial plants emit volatiles into the atmosphere to attract both pollinators and the enemies of herbivores, for defense. Phalaenopsis bellina is a scented orchid species in which the main scent components are monoterpenes, including linalool and geraniol, and their derivatives. Here, we investigated whether ABC transporters are involved in floral scent emission. We carried out whole-genome identification of ABC transporter-related genes using four floral transcriptomics libraries of P. bellina. We identified 86 ABC subfamily G genes related to terpenoid transport. After comparing the gene expression patterns of P. bellina with that of Phalaenopsis aphrodite subsp. formosana, a scentless species, followed by gene-to-gene correlation analysis, PbABCG1 and PbABCG2 were selected. The temporal expression of both PbABCG1 and PbABCG2 was highly correlated with that of the key enzyme PbGDPS and the major transcription factor PbbHLH4 in monoterpene biosynthesis, with optimal expression on day 5 post-anthesis. Spatial gene expression analysis showed that PbABCG1 was highly expressed in sepals, whereas PbABCG2 was expressed in the lip. Subcellular localization with a GFP fusion protein revealed that both PbABCG1 and PbABCG2 are cytoplasmic membrane proteins. Co-downregulation of PbABCG1 and PbABCG2 using both double-strand RNA interference and tobacco rattle virus-based gene silencing led to a significant decrease in monoterpene emission, accompanied by an increase in the internal monoterpene pools. Furthermore, ectopic expression of PbABCG1 and PbABCG2 in an ABC16- mutant yeast strain rescued its tolerance to geraniol. Altogether, our results indicate that PbABCG1 and PbABCG2 play substantial roles in monoterpene transport/emission in P. bellina floral scent.
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Affiliation(s)
- Ya-Lan Chang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Xuan-Zhou Kuo
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shao-Ting Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Mei-Fen Jeng
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hsin-Hung Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
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11
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Liu H, Du B, Ma X, Wang Y, Cheng N, Zhang Y. Overexpression of major latex protein 423 (NtMLP423) enhances the chilling stress tolerance in Nicotiana tabacum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111604. [PMID: 36709884 DOI: 10.1016/j.plantsci.2023.111604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Chilling stress impedes plant growth and hinders crop development and productivity. In this study, we identified the major latex protein (MLP) in tobacco (NtMLP423) and examined its roles in chilling resistance. NtMLP423 expression was considerably upregulated in response to chilling stress. NtMLP423 function was assessed and compared in plants with overexpression and antisense characteristics. Under chilling stress, plants with overexpression characteristics grew better than wild-type and antisense plants. NtMLP423 overexpression reduced membrane lipid damage, increased antioxidant enzyme activity, and reduced reactive oxygen species (ROS) accumulation under chilling stress. Here, we screened for the first time the upstream transcription factor NtMYB108, which regulates NtMLP423 expression under chilling stress. The NtMYB108 transcription factor directly binds to the NtMLP423 promoter and improves NtMLP423 resistance to chilling stress. Subjecting NtMYB018 to virus-induced gene silencing reduced chilling stress tolerance. Overall, NtMLP423 overexpression enhances chilling stress tolerance, while its suppression has the opposite effect.
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Affiliation(s)
- Heng Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China; Linyi University, Linyi 276005, Shandong, PR China
| | - Bingyang Du
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Xiaocen Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Nini Cheng
- Linyi University, Linyi 276005, Shandong, PR China.
| | - Yuanhu Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
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12
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Fernandez JC, Gilroy S. Imaging systemic calcium response and its molecular dissection using virus-induced gene silencing. Methods Enzymol 2023; 680:439-459. [PMID: 36710022 DOI: 10.1016/bs.mie.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Many biotic and abiotic stimuli arrive locally on the plant. For example, attack by an insect or invasion by a fungal pathogen generally starts with a single leaf. However, the responses that are then elicited are often systemic, triggering effects throughout the entire plant body. One of the rapid signaling systems that helps coordinate these plant-wide response networks is changes in cytoplasmic Ca2+ that rapidly propagate throughout the plant. These Ca2+ signals are readily visualized using plants expressing green fluorescent protein-based Ca2+-sensitive bioreporters, such as those of the GCaMP and GECO families. Dissecting the underlying molecular machinery behind this systemic spread of information is often approached by imaging the Ca2+ response in mutants in candidate genes. Introducing the GFP sensor into the relevant genetic backgrounds and then selecting lines usable for imaging can be very time consuming. An alternative, more rapid approach to screening these candidates is through virus-induced gene silencing (VIGS), where target genes are suppressed in the wild-type bioreporter expressing plants. This chapter describes how to generate VIGS constructs targeted to candidate genes and then how to visualize wound-induced, systemic Ca2+ signaling in the VIGS suppressed plants.
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Affiliation(s)
| | - Simon Gilroy
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States.
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13
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Establishment of a Virus-Induced Gene-Silencing (VIGS) System in Tea Plant and Its Use in the Functional Analysis of CsTCS1. Int J Mol Sci 2022; 24:ijms24010392. [PMID: 36613837 PMCID: PMC9820744 DOI: 10.3390/ijms24010392] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Tea (Camellia sinensis [L.] O. Kuntze) is an important global economic crop and is considered to enhance health. However, the functions of many genes in tea plants are unknown. Virus-induced gene silencing (VIGS) mediated by tobacco rattle virus (TRV) is an effective tool for the analysis of gene functions, although this method has rarely been reported in tea plants. In this study, we established an effective VIGS-mediated gene knockout technology to understand the functional identification of large-scale genomic sequences in tea plants. The results showed that the VIGS system was verified by detecting the virus and using a real-time quantitative reverse transcription PCR (qRT-PCR) analysis. The reporter gene CsPOR1 (protochlorophyllide oxidoreductase) was silenced using the vacuum infiltration method, and typical photobleaching and albino symptoms were observed in newly sprouted leaves at the whole plant level of tea after infection for 12 d and 25 d. After optimization, the VIGS system was successfully used to silence the tea plant CsTCS1 (caffeine synthase) gene. The results showed that the relative caffeine content was reduced 6.26-fold compared with the control, and the level of expression of CsPOR1 decreased by approximately 3.12-fold in plants in which CsPOR1 was silenced. These results demonstrate that VIGS can be quickly and efficiently used to analyze the function of genes in tea plants. The successful establishment of VIGS could eliminate the need for tissue culture by providing an effective method to study gene function in tea plants and accelerate the process of functional genome research in tea.
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Wang Y, Yuan S, Shao C, Zhu W, Xiao D, Zhang C, Hou X, Li Y. BcOPR3 Mediates Defense Responses to Biotrophic and Necrotrophic Pathogens in Arabidopsis and Non-heading Chinese Cabbage. PHYTOPATHOLOGY 2022; 112:2523-2537. [PMID: 35852468 DOI: 10.1094/phyto-02-22-0049-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In plants, the salicylic acid (SA) and jasmonic acid (JA) signaling pathways usually mediate the defense response to biotrophic and necrotrophic pathogens, respectively. Our previous work showed that after non-heading Chinese cabbage (NHCC) was infected with the biotrophic pathogen Hyaloperonospora parasitica, expression of the JA biosynthetic gene BcOPR3 is induced; however, its molecular mechanism remains unclear. Here, we overexpressed BcOPR3 in Arabidopsis and silenced BcOPR3 in NHCC001 plants to study the defensive role of BcOPR3 in plants against pathogen invasion. The results showed that overexpression of BcOPR3 increased the susceptibility of Arabidopsis to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) but enhanced its resistance to Botrytis cinerea. BcOPR3-silenced NHCC001 plants with a 50% reduction in BcOPR3 expression increased their resistance to downy mildew by reducing the hyphal density and spores of H. parasitica. In addition, BcOPR3-partly silenced NHCC001 plants were also resistant to B. cinerea, which could be the result of a synergistic effect of JA and SA. These findings indicate a complicated role of BcOPR3 in the mediating defense responses to biotrophic and necrotrophic pathogens.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuilin Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Cen Shao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weitong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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15
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Long Y, Chen Q, Qu Y, Liu P, Jiao Y, Cai Y, Deng X, Zheng K. Identification and functional analysis of PIN family genes in Gossypium barbadense. PeerJ 2022; 10:e14236. [PMID: 36275460 PMCID: PMC9586078 DOI: 10.7717/peerj.14236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023] Open
Abstract
Background PIN proteins are an important class of auxin polar transport proteins that play an important regulatory role in plant growth and development. However, their characteristics and functions have not been identified in Gossypium barbadense. Methods PIN family genes were identified in the cotton species G. barbadense, Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, and detailed bioinformatics analyses were conducted to explore the roles of these genes in G. barbadense using transcriptome data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) technology. Functional verification of the genes was performed using virus-induced gene silencing (VIGS) technology. Results A total of 138 PIN family genes were identified in the four cotton species; the genes were divided into seven subgroups. GbPIN gene family members were widely distributed on 20 different chromosomes, and most had repeated duplication events. Transcriptome analysis showed that some genes had differential expression patterns in different stages of fiber development. According to 'PimaS-7' and '5917' transcript component association analysis, the transcription of five genes was directly related to endogenous auxin content in cotton fibers. qRT-PCR analysis showed that the GbPIN7 gene was routinely expressed during fiber development, and there were significant differences among materials. Transient silencing of the GbPIN7 gene by VIGS led to significantly higher cotton plant growth rates and significantly lower endogenous auxin content in leaves and stems. This study provides comprehensive analyses of the roles of PIN family genes in G. barbadense and their expression during cotton fiber development. Our results will form a basis for further PIN auxin transporter research.
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Affiliation(s)
- Yilei Long
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Pengfei Liu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Yang Jiao
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Yongsheng Cai
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiaojuan Deng
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China,Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China,Postdoctoral Research Station, Xinjiang Agricultural University, Urumqi, Xinjiang, China
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16
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Wang Y, Zhao J, Deng X, Wang P, Geng S, Gao W, Guo P, Chen Q, Li C, Qu Y. Genome-wide analysis of serine carboxypeptidase-like protein (SCPL) family and functional validation of Gh_SCPL42 unchromosome conferring cotton Verticillium der Verticillium wilt stress in Gossypium hirsutum. BMC PLANT BIOLOGY 2022; 22:421. [PMID: 36045341 PMCID: PMC9434971 DOI: 10.1186/s12870-022-03804-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Serine carboxypeptidase-like protein (SCPL) plays an important role in response to stress in plant. However, our knowledge of the function of the SCPL gene family is limited. RESULTS In this study, a comprehensive and systematic analysis of SCPL gene family was conducted to explore the phylogeny and evolution of the SCPL gene in Gossypium hirsutum. The phenotype and molecular mechanism of silencing of the Gh_SCPL42 under Verticillium wilt stress was also studied. Our results showed that 96 SCPL genes were observed in genome of G. hirsutum, which distributed on 25 chromosomes and most of them were located in the nucleus. The phylogenetic tree analysis showed that members of SCPL gene family can be divided into three subgroups in G. hirsutum, which are relatively conservative in evolution. SCPL gene has a wide range of tissue expression types in G. hirsutum. Promoter analysis showed that the most cis-acting elements related to MeJA and ABA were contained. Through RNA-seq combined with genotyping, it was found that 11 GhSCPL genes not only had significant expression changes during Verticillium wilt stress but also had differential SNPs in the upstream, downstream, exonic or intronic regions. The expression of these 11 genes in the resistant (Zhongzhimian 2) and susceptible (Junmian 1) materials was further analyzed by qRT-PCR, it was found that 6 genes showed significant expression differences in the two materials. Among them, Gh_SCPL42 has the most obvious expression change. Furthermore, virus-induced gene silencing (VIGS) showed necrosis and yellowing of leaves and significantly higher disease severity index (DSI) and disease severity rate (DSR) values in VIGS plants than in control silenced Gh_SCPL42 plants. Moreover, the expression levels of genes related to the SA and JA pathways were significantly downregulated. These results show that Gh_SCPL42 might improve resistance to Verticillium wilt through the SA and JA pathways in G. hirsutum. CONCLUSION In conclusion, our findings indicated that Gh_SCPL42 gene plays an important role in resistance to Verticillium wilt in cotton. It was provided an important theoretical basis for further research on the function of SCPL gene family and the molecular mechanism of resistance to Verticillium wilt in cotton.
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Affiliation(s)
- Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Peng Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Peipei Guo
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Chunping Li
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830052, China.
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
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Zhou P, Dang J, Shi Z, Shao Y, Sang M, Dai S, Yue W, Liu C, Wu Q. Identification and characterization of a novel gene involved in glandular trichome development in Nepeta tenuifolia. FRONTIERS IN PLANT SCIENCE 2022; 13:936244. [PMID: 35968082 PMCID: PMC9372485 DOI: 10.3389/fpls.2022.936244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Nepeta tenuifolia is a medicinal plant rich in terpenoids and flavonoids with antiviral, immunoregulatory, and anti-inflammatory activities. The peltate glandular trichome (PGT) is a multicellular structure considered to be the primary storage organ for monoterpenes; it may serve as an ideal model for studying cell differentiation and the development of glandular trichomes (GTs). The genes that regulate the development of GTs have not yet been well studied. In this study, we identified NtMIXTA1, a GT development-associated gene from the R2R3 MYB SBG9 family. NtMIXTA1 overexpression in tobacco resulted in the production of longer and denser GTs. Virus-induced gene silencing of NtMIXTA1 resulted in lower PGT density, a significant reduction in monoterpene concentration, and the decreased expression of genes related to monoterpene biosynthesis. Comparative transcriptome and widely targeted metabolic analyses revealed that silencing NtMIXTA1 significantly influenced the expression of genes, and the production of metabolites involved in the biosynthesis of terpenoids, flavonoids, and lipids. This study provides a solid foundation describing a mechanism underlying the regulation of GT development. In addition, this study further deepens our understanding of the regulatory networks involved in GT development and GT development-associated metabolite flux, as well as provides valuable reference data for studying plants with a high medicinal value without genetic transformation.
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Affiliation(s)
- Peina Zhou
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Jingjie Dang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Zunrui Shi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Yongfang Shao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Mengru Sang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Shilin Dai
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Wei Yue
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Chanchan Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
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Identification of CDPK Gene Family in Solanum habrochaites and Its Function Analysis under Stress. Int J Mol Sci 2022; 23:ijms23084227. [PMID: 35457042 PMCID: PMC9031491 DOI: 10.3390/ijms23084227] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Tomato is an important vegetable crop. In the process of tomato production, it will encounter abiotic stress, such as low temperature, drought, and high salt, and biotic stress, such as pathogen infection, which will seriously affect the yield of tomato. Calcium-dependent protein kinase (CDPK) is a class of major calcium signal receptor which has an important regulatory effect on the perception and decoding of calcium signals. CDPK plays a key role in many aspects of plant growth, such as the elongation of pollen tubes, plant growth, and response to biotic and abiotic stress. While some studies have concentrated on Arabidopsis and pepper, Solanum habrochaites is a wild species relative of cultivated tomato and there is no report on CDPK in Solanum habrochaites to date. Using tomato genomic data, this study identified 33 members of the CDPK gene family. Evolutionary analysis divides family members into four Asian groups, of which the CDPK family members have 11 gene replication pairs. Subcellular location analysis showed that most proteins were predicted to be located in the cytoplasm, and less protein existed on the cell membrane. Not all CDPK family members have a transmembrane domain. Cis regulatory elements relating to light, hormones, and drought stress are overrepresented in the promoter region of the CDPK genes in Solanum habrochaites. The expression levels of each gene under biotic stress and abiotic stress were quantified by qRT-PCR. The results showed that members of the CDPK family in Solanum habrochaites respond to different biotic and abiotic stresses. Among them, the expression of ShCDPK6 and ShCDPK26 genes change significantly. ShCDPK6 and ShCDPK26 genes were silenced using VIGS (virus-induced gene silencing), and the silenced plants illustrated reduced stress resistance to Botrytis cinerea, cold, and drought stress. The results of this study will provide a basis for the in-depth study of the CDPK gene family in Solanum habrochaites, laying the foundation for further analysis of the function of the gene family.
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Han W, Zhao J, Deng X, Gu A, Li D, Wang Y, Lu X, Zu Q, Chen Q, Chen Q, Zhang J, Qu Y. Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population of Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2022; 13:815643. [PMID: 35371113 PMCID: PMC8965654 DOI: 10.3389/fpls.2022.815643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 05/16/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive diseases in cotton (Gossypium spp.) production, and use of resistant cultivars is the most cost-effective method managing the disease. To understand the genetic basis of cotton resistance to FOV race 7 (FOV7), this study evaluated a recombinant inbred line (RIL) population of 110 lines of G. barbadense from a cross between susceptible Xinhai 14 and resistant 06-146 in eight tests and constructed a high-density genetic linkage map with resequencing-based 933,845 single-nucleotide polymorphism (SNP) markers covering a total genetic distance of 2483.17 cM. Nine quantitative trait loci (QTLs) for FOV7 resistance were identified, including qFOV7-D03-1 on chromosome D03 in two tests. Through a comparative analysis of gene expression and DNA sequence for predicted genes within the QTL region between the two parents and selected lines inoculated with FOV7, GB_D03G0217 encoding for a calmodulin (CaM)-like (CML) protein was identified as a candidate gene. A further analysis confirmed that the expression of GB_D03G0217 was suppressed, leading to increased disease severity in plants of the resistant parent with virus induced gene silencing (VIGS).
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Affiliation(s)
- Wanli Han
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Aixing Gu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Duolu Li
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaoshuang Lu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Qianli Zu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Qin Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
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20
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Helderman TA, Deurhof L, Bertran A, Richard MMS, Kormelink R, Prins M, Joosten MHAJ, van den Burg HA. Members of the ribosomal protein S6 (RPS6) family act as pro-viral factor for tomato spotted wilt orthotospovirus infectivity in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2022; 23:431-446. [PMID: 34913556 PMCID: PMC8828452 DOI: 10.1111/mpp.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 05/07/2023]
Abstract
To identify host factors for tomato spotted wilt orthotospovirus (TSWV), a virus-induced gene silencing (VIGS) screen using tobacco rattle virus (TRV) was performed on Nicotiana benthamiana for TSWV susceptibility. To rule out any negative effect on the plants' performance due to a double viral infection, the method was optimized to allow screening of hundreds of clones in a standardized fashion. To normalize the results obtained in and between experiments, a set of controls was developed to evaluate in a consist manner both VIGS efficacy and the level of TSWV resistance. Using this method, 4532 random clones of an N. benthamiana cDNA library were tested, resulting in five TRV clones that provided nearly complete resistance against TSWV. Here we report on one of these clones, of which the insert targets a small gene family coding for the ribosomal protein S6 (RPS6) that is part of the 40S ribosomal subunit. This RPS6 family is represented by three gene clades in the genome of Solanaceae family members, which were jointly important for TSWV susceptibility. Interestingly, RPS6 is a known host factor implicated in the replication of different plant RNA viruses, including the negative-stranded TSWV and the positive-stranded potato virus X.
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Affiliation(s)
- Tieme A. Helderman
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
| | - Laurens Deurhof
- Laboratory of PhytopathologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - André Bertran
- Laboratory of VirologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - Manon M. S. Richard
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
| | - Richard Kormelink
- Laboratory of VirologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - Marcel Prins
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
- KeyGene N.V.WageningenNetherlands
| | | | - Harrold A. van den Burg
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
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21
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Murai H, Mochizuki T. Virus-Induced Gene Silencing in Chrysanthemum seticuspe Using the Tomato Aspermy Virus Vector. PLANTS (BASEL, SWITZERLAND) 2022; 11:430. [PMID: 35161409 PMCID: PMC8838493 DOI: 10.3390/plants11030430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Chrysanthemum is one of the most economically important flowers globally due to its high ornamental value. In recent years, a large percentage of the Chrysanthemum seticuspe genome has been determined, making this species useful as a model chrysanthemum plant. To fully utilize the genome's information, efficient and rapid gene functional analysis methods are needed. In this study, we optimized the tomato aspermy virus (TAV) vector for virus-induced gene silencing (VIGS) in C. seticuspe. Conventional plant virus inoculation methods, such as the mechanical inoculation of viral RNA transcripts and agroinoculation into leaves, did not achieve successful TAV infections in C. seticuspe, but vacuum infiltration into sprouts was successful without symptoms. The TAV vector harboring 100 nucleotides of the phytoene desaturase (PDS) gene caused photobleaching phenotypes and a reduction in CsPDS expression in C. seticuspe. To our knowledge, this is the first report of VIGS in chrysanthemums.
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22
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Tobacco Rattle Virus as a Tool for Rapid Reverse-Genetics Screens and Analysis of Gene Function in Cannabis sativa L. PLANTS 2022; 11:plants11030327. [PMID: 35161308 PMCID: PMC8838890 DOI: 10.3390/plants11030327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/19/2022]
Abstract
Medical cannabis (Cannabis sativa L.) is quickly becoming a central agricultural crop as its production has continued to increase globally. The recent release of the cannabis reference genomes provides key genetic information for the functional analysis of cannabis genes. Currently, however, the established tools for in vivo gene functional analysis in cannabis are very limited. In this study, we investigated the use of the tobacco rattle virus (TRV) as a possible tool for virus-induced gene silencing (VIGS) and virus-aided gene expression (VAGE). Using leaf photobleaching as a visual marker of PHYTOENE DESATURASE (PDS) silencing, we found that VIGS was largely restricted to the agro-infiltrated leaves. However, when agro-infiltration was performed under vacuum, VIGS increased dramatically, which resulted in intense PDS silencing and an increased photobleaching phenotype. The suitability of TRV as a vector for virus-aided gene expression (VAGE) was demonstrated by an analysis of DsRed fluorescence protein. Interestingly, a DsRed signal was also observed in glandular trichomes in TRV2-DsRed-infected plants, which suggests the possibility of trichome-related gene function analysis. These results indicate that TRV, despite its limited spread, is an attractive vector for rapid reverse-genetics screens and for the analysis of gene function in cannabis.
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23
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Paudel L, Kerr S, Prentis P, Tanurdžić M, Papanicolaou A, Plett JM, Cazzonelli CI. Horticultural innovation by viral-induced gene regulation of carotenogenesis. HORTICULTURE RESEARCH 2022; 9:uhab008. [PMID: 35043183 PMCID: PMC8769041 DOI: 10.1093/hr/uhab008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/31/2021] [Accepted: 09/24/2021] [Indexed: 06/14/2023]
Abstract
Multipartite viral vectors provide a simple, inexpensive and effective biotechnological tool to transiently manipulate (i.e. reduce or increase) gene expression in planta and characterise the function of genetic traits. The development of virus-induced gene regulation (VIGR) systems usually involve the targeted silencing or overexpression of genes involved in pigment biosynthesis or degradation in plastids, thereby providing rapid visual assessment of success in establishing RNA- or DNA-based VIGR systems in planta. Carotenoids pigments provide plant tissues with an array of yellow, orange, and pinkish-red colours. VIGR-induced transient manipulation of carotenoid-related gene expression has advanced our understanding of carotenoid biosynthesis, regulation, accumulation and degradation, as well as plastid signalling processes. In this review, we describe mechanisms of VIGR, the importance of carotenoids as visual markers of technology development, and knowledge gained through manipulating carotenogenesis in model plants as well as horticultural crops not always amenable to transgenic approaches. We outline how VIGR can be utilised in plants to fast-track the characterisation of gene function(s), accelerate fruit tree breeding programs, edit genomes, and biofortify plant products enriched in carotenoid micronutrients for horticultural innovation.
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Affiliation(s)
- Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Stephanie Kerr
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, 2 George Street, Brisbane City, QLD 4000, Australia
- School of Biology and Environmental Sciences, Faculty of Science,
Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, Australia
| | - Peter Prentis
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, 2 George Street, Brisbane City, QLD 4000, Australia
- School of Biology and Environmental Sciences, Faculty of Science,
Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, Australia
| | - Miloš Tanurdžić
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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24
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Sharma VK, Marla S, Zheng W, Mishra D, Huang J, Zhang W, Morris GP, Cook DE. CRISPR guides induce gene silencing in plants in the absence of Cas. Genome Biol 2022; 23:6. [PMID: 34980227 PMCID: PMC8722000 DOI: 10.1186/s13059-021-02586-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation, and expanded function including antiviral immunity. RESULTS Here, we report the use of CRISPR-Cas13 in plants to reduce both viral and endogenous RNA. Unexpectedly, we observe that crRNA designed to guide Cas13 could, in the absence of the Cas13 protein, cause substantial reduction in RNA levels as well. We demonstrate Cas13-independent guide-induced gene silencing (GIGS) in three plant species, including stable transgenic Arabidopsis. Small RNA sequencing during GIGS identifies the production of small RNA that extend beyond the crRNA expressed sequence in samples expressing multi-guide crRNA. Additionally, we demonstrate that mismatches in guide sequences at position 10 and 11 abolish GIGS. Finally, we show that GIGS is elicited by guides that lack the Cas13 direct repeat and can extend to Cas9 designed crRNA of at least 28 base pairs, indicating that GIGS can be elicited through a variety of guide designs and is not dependent on Cas13 crRNA sequences or design. CONCLUSIONS Collectively, our results suggest that GIGS utilizes endogenous RNAi machinery despite the fact that crRNA are unlike canonical triggers of RNAi such as miRNA, hairpins, or long double-stranded RNA. Given similar evidence of Cas13-independent silencing in an insect system, it is likely GIGS is active across many eukaryotes. Our results show that GIGS offers a novel and flexible approach to RNA reduction with potential benefits over existing technologies for crop improvement and functional genomics.
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Affiliation(s)
| | - Sandeep Marla
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Wenguang Zheng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Divya Mishra
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jun Huang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Wei Zhang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - David Edward Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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25
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Ding Y, Chen Y, Yan B, Liao H, Dong M, Meng X, Wan H, Qian W. Host-Induced Gene Silencing of a Multifunction Gene Sscnd1 Enhances Plant Resistance Against Sclerotinia sclerotiorum. Front Microbiol 2021; 12:693334. [PMID: 34690946 PMCID: PMC8531507 DOI: 10.3389/fmicb.2021.693334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Sclerotinia sclerotiorum is a devastating necrotrophic fungal pathogen and has a substantial economic impact on crop production worldwide. Magnaporthe appressoria-specific (MAS) proteins have been suggested to be involved in the appressorium formation in Magnaporthe oryzae. Sscnd1, an MAS homolog gene, is highly induced at the early infection stage of S. sclerotiorum. Knock-down the expression of Sscnd1 gene severely reduced the virulence of S. sclerotiorum on intact rapeseed leaves, and their virulence was partially restored on wounded leaves. The Sscnd1 gene-silenced strains exhibited a defect in compound appressorium formation and cell integrity. The instantaneous silencing of Sscnd1 by tobacco rattle virus (TRV)-mediated host-induced gene silencing (HIGS) resulted in a significant reduction in disease development in tobacco. Three transgenic HIGS Arabidopsis lines displayed high levels of resistance to S. sclerotiorum and decreased Sscnd1 expression. Production of specific Sscnd1 siRNA in transgenic HIGS Arabidopsis lines was confirmed by stem-loop qRT-PCR. This study revealed that the compound appressorium-related gene Sscnd1 is required for cell integrity and full virulence in S. sclerotiorum and that Sclerotinia stem rot can be controlled by expressing the silencing constructs of Sscnd1 in host plants.
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Affiliation(s)
- Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Yangui Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Baoqin Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Hongmei Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Mengquan Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Xinran Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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26
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Shi G, Hao M, Tian B, Cao G, Wei F, Xie Z. A Methodological Advance of Tobacco Rattle Virus-Induced Gene Silencing for Functional Genomics in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:671091. [PMID: 34149770 PMCID: PMC8212136 DOI: 10.3389/fpls.2021.671091] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/10/2021] [Indexed: 05/19/2023]
Abstract
As a promising high-throughput reverse genetic tool in plants, virus-induced gene silencing (VIGS) has already begun to fulfill some of this promise in diverse aspects. However, review of the technological advancements about widely used VIGS system, tobacco rattle virus (TRV)-mediated gene silencing, needs timely updates. Hence, this article mainly reviews viral vector construction, inoculation method advances, important influential factors, and summarizes the recent applications in diverse plant species, thus providing a better understanding and advice for functional gene analysis related to crop improvements.
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Affiliation(s)
- Gongyao Shi
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Mengyuan Hao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Baoming Tian
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Gangqiang Cao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Fang Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhengqing Xie
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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27
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Carey S, Higuera‐Díaz M, Mankowski P, Rocca A, Hall JC. Virus-induced gene silencing as a tool for functional studies in Cleome violacea. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311435. [PMID: 34141499 PMCID: PMC8202831 DOI: 10.1002/aps3.11435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
PREMISE Cleomaceae is emerging as a promising family to investigate a wide range of phenomena, such as C4 photosynthesis and floral diversity. However, functional techniques are lacking for elucidating this diversity. Herein, we establish virus-induced gene silencing (VIGS) as a method of generating functional data for Cleome violacea, bolstering Cleomaceae as a model system. METHODS We leveraged the sister relationship of Cleomaceae and Brassicaceae by using constructs readily available for Arabidopsis thaliana to provide initial information about the feasibility of VIGS in C. violacea. We then developed endogenous constructs to optimize VIGS efficiency and viability for fruit development. RESULTS PHYTOENE DESATURASE was successfully downregulated in C. violacea using both heterologous and endogenous constructs. The endogenous construct had the highest degree of downregulation, with many plants displaying strong photobleaching. FRUITFULL-treated plants were also successfully downregulated, with a high rate of survival but less effective silencing; only a small percentage of survivors showed a strong phenotype. DISCUSSION Our optimized VIGS protocol in C. violacea enables functional gene analyses at different developmental stages. Additionally, C. violacea is amenable to heterologous knockdown, which suggests that a first pass using non-endogenous constructs is a possible route to test additional species of Cleomaceae.
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Affiliation(s)
- Shane Carey
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Peter Mankowski
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Department of SurgeryUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Alexandra Rocca
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Administration BuildingUniversity of AlbertaEdmontonAlbertaCanada
| | - Jocelyn C. Hall
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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28
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Atsumi G, Matsuo K, Fukuzawa N, Matsumura T. Virus-Mediated Targeted DNA Methylation Illuminates the Dynamics of Methylation in an Endogenous Plant Gene. Int J Mol Sci 2021; 22:4125. [PMID: 33923780 PMCID: PMC8073618 DOI: 10.3390/ijms22084125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation maintains genome stability and regulates gene expression in plants. RNA-directed DNA methylation (RdDM) is critical for appropriate methylation. However, no efficient tools are available for the investigation of the functions of specific DNA methylation. In this study, the cucumber mosaic virus vector was used for targeted DNA methylation. Methylation was rapidly induced but gradually decreased from the 3' end of the target endogenous sequence in Nicotiana benthamiana, suggesting a mechanism to protect against the ectopic introduction of DNA methylation. Increasing 24-nt siRNAs blocked this reduction in methylation by down-regulating DCL2 and DCL4. RdDM relies on the sequence identity between RNA and genomic DNA; however, this identity does not appear to be the sole determinant for efficient DNA methylation. The current findings provide new insight into the regulation of DNA methylation and promote additional effort to develop efficient targeted DNA methylation in plants.
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29
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Abstract
Virus-induced gene silencing (VIGS) is a versatile tool for genetic studies that has been applied to a variety of plant species. With the advent of more accessible genomic and transcriptomic technology applied to an increasing range of plants, tools such as VIGS are being adapted to more non-model plants to explore genes relevant to agriculture and chemical discovery. In this protocol, we adapted VIGS technology to target genes in Nepeta cataria (catnip) and Nepeta mussinii (catmint). These plants carry biochemical and economical value for their production of nepetalactone, an iridoid which provokes a strong reaction in both house cats and aphids. We describe a method to target magnesium chelatase subunit H (CHlH), a gene often targeted as a visual marker for VIGS. Furthermore, we describe a method to simultaneously target two genes in a single plant, which aids in the study of genes found in key biochemical steps in the production of nepetalactone. This approach, which was successfully applied in two members of the Lamiaceae family (mint), could be adapted to other members of the mint family with economical and chemical value.
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30
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Wang Z, Zhang L, Dong C, Guo J, Jin L, Wei P, Li F, Zhang X, Wang R. Characterization and functional analysis of phytoene synthase gene family in tobacco. BMC PLANT BIOLOGY 2021; 21:32. [PMID: 33413114 PMCID: PMC7791662 DOI: 10.1186/s12870-020-02816-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/22/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Carotenoids play important roles in photosynthesis, hormone signaling, and secondary metabolism. Phytoene synthase (PSY) catalyzes the first step of the carotenoid biosynthetic pathway. In this study, we aimed to characterize the PSY genes in tobacco and analyze their function. RESULTS In this study, we identified three groups of PSY genes, namely PSY1, PSY2, and PSY3, in four Nicotiana species; phylogenetic analysis indicated that these genes shared a high similarity with those in tomato but not with those in monocots such as rice and maize. The expression levels of PSY1 and PSY2 were observed to be highest in leaves compared to other tissues, and they could be elevated by treatment with certain phytohormones and exposure to strong light. No PSY3 expression was detected under these conditions. We constructed virus-induced PSY1 and PSY2 silencing in tobacco and found that the newly emerged leaves in these plants were characterized by severe bleaching and markedly decreased carotenoid and chlorophyll content. Thylakoid membrane protein complex levels in the gene-silenced plants were also less than those in the control plants. The chlorophyll fluorescence parameters such as Fv/Fm, ΦPSII, qP, and NPQ, which reflect photosynthetic system activities, of the gene-silenced plants were also significantly decreased. We further performed RNA-Seq and metabonomics analysis between gene-silenced tobacco and control plants. RNA-Seq results showed that abiotic stress, isoprenoid compounds, and amino acid catabolic processes were upregulated, whereas the biosynthesis of cell wall components was downregulated. Metabolic analysis results were consistent with the RNA-Seq. We also found the downstream genes in carotenoid biosynthesis pathways were upregulated, and putative transcription factors that regulate carotenoid biosynthesis were identified. CONCLUSIONS Our results suggest that PSY can regulate carotenoid contents not only by controlling the first biosynthesis step but also by exerting effects on the expression of downstream genes, which would thereby affect photosynthetic activity. Meanwhile, PSY may affect other processes such as amino acid catabolism and cell wall organization. The information we report here may aid further research on PSY genes and carotenoid biosynthesis.
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Affiliation(s)
- Zhaojun Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lin Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, 650231, Yunnan, China
| | - Chen Dong
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Jinggong Guo
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Lifeng Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Pan Wei
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Feng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Xiaoquan Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Ran Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
- School of Life Sciences, School of Agricultural Sciences, Zhengzhou University, No. 100 Science Road, Gaoxin Distract, Zhengzhou, 450001, Henan, China.
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31
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Murphree C, Kim S, Karre S, Samira R, Balint‐Kurti P. Use of virus-induced gene silencing to characterize genes involved in modulating hypersensitive cell death in maize. MOLECULAR PLANT PATHOLOGY 2020; 21:1662-1676. [PMID: 33037769 PMCID: PMC7694674 DOI: 10.1111/mpp.12999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 09/04/2020] [Indexed: 05/22/2023]
Abstract
Plant disease resistance proteins (R-proteins) detect specific pathogen-derived molecules, triggering a defence response often including a rapid localized cell death at the point of pathogen penetration called the hypersensitive response (HR). The maize Rp1-D21 gene encodes a protein that triggers a spontaneous HR causing spots on leaves in the absence of any pathogen. Previously, we used fine mapping and functional analysis in a Nicotiana benthamiana transient expression system to identify and characterize a number of genes associated with variation in Rp1-D21-induced HR. Here we describe a system for characterizing genes mediating HR, using virus-induced gene silencing (VIGS) in a maize line carrying Rp1-D21. We assess the roles of 12 candidate genes. Three of these genes, SGT1, RAR1, and HSP90, are required for HR induced by a number of R-proteins across several plant-pathogen systems. We confirmed that maize HSP90 was required for full Rp1-D21-induced HR. However, suppression of SGT1 expression unexpectedly increased the severity of Rp1-D21-induced HR while suppression of RAR1 expression had no measurable effect. We confirmed the effects on HR of two genes we had previously validated in the N. benthamiana system, hydroxycinnamoyltransferase and caffeoyl CoA O-methyltransferase. We further showed the suppression the expression of two previously uncharacterized, candidate genes, IQ calmodulin binding protein (IQM3) and vacuolar protein sorting protein 37, suppressed Rp1-D21-induced HR. This approach is an efficient way to characterize the roles of genes modulating the hypersensitive defence response and other dominant lesion phenotypes in maize.
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Affiliation(s)
- Colin Murphree
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Saet‐Byul Kim
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Shailesh Karre
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Rozalynne Samira
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Fiber and Biopolymer Research Institute (FBRI)Department of Plant and Soil ScienceTexas Tech UniversityTexasUSA
| | - Peter Balint‐Kurti
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Plant Science Research UnitUSDA‐ARSRaleighNorth CarolinaUSA
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Xiao Z, Xing M, Liu X, Fang Z, Yang L, Zhang Y, Wang Y, Zhuang M, Lv H. An efficient virus-induced gene silencing (VIGS) system for functional genomics in Brassicas using a cabbage leaf curl virus (CaLCuV)-based vector. PLANTA 2020; 252:42. [PMID: 32870402 DOI: 10.1007/s00425-020-03454-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
CaLCuV-based VIGS effectively works in cabbage and contributes to efficient functional genomics research in Brassica crop species. Virus-induced gene silencing (VIGS), a posttranscriptional gene silencing method, is an effective technique for analysing the functions of genes in plants. However, no VIGS vectors have been available for Brassica oleracea until now. Here, tobacco rattle virus (TRV), pTYs and cabbage leaf curl virus (CaLCuV) gene-silencing vectors (PCVA/PCVB) were chosen to improve the VIGS system in cabbage using the phytoene desaturase (PDS) gene as an efficient visual indicator of VIGS. We successfully silenced the expression of PDS and observed photobleaching phenomena in cabbage in response to pTYs and CaLCuV, with the latter being more easy to operate and less expensive. The parameters potentially affecting the silencing efficiency of VIGS by CaLCuV in cabbage, including the targeting fragment strategy, inoculation method and incubation temperature, were then compared. The optimized CaLCuV-based VIGS system involves the following: an approximately 500 bp insert sequence, an Agrobacterium OD600 of 1.0, use of the vacuum osmosis method applied at the bud stage, and an incubation temperature of 22 °C. Using these parameters, we achieved a stable silencing efficiency of 65%. To further test the effectiveness of the system, we selected the Mg-chelatase H subunit (ChlH) gene in cabbage and knocked down its expression, and we observed yellow leaves, as expected. We successfully applied the CaLCuV-based VIGS system to two other representative Brassica crop species, B. rapa and B. nigra, and thus expanded the application scope of this system. Our VIGS system described here will contribute to efficient functional genomics research in Brassica crop species.
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Affiliation(s)
- Zhiliang Xiao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Miaomiao Xing
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Xing Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China.
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun Nandajie Street, Beijing, 100081, China.
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Nishii K, Fei Y, Hudson A, Möller M, Molnar A. Virus-induced Gene Silencing in Streptocarpus rexii (Gesneriaceae). Mol Biotechnol 2020; 62:317-325. [PMID: 32146689 DOI: 10.1007/s12033-020-00248-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many members of the family Gesneriaceae are cultivated as ornamental plants, including Cape primrose (Streptocarpus) species. The range of plant architecture found in this genus has also made it a model to study leaf and meristem development and their evolution. However, the lack of tools to study gene functions through reverse genetics in Streptocarpus has limited the exploitation of its genetic potential. To aid functional genomic studies in Streptocarpus rexii, we sought to investigate virus-induced gene silencing (VIGS). Using the broad host range Tobacco Rattle Virus (TRV) to target the PHYTOENE DESATURASE (PDS) gene of S. rexii, we show that infection with sap from Nicotiana benthamiana triggered VIGS efficiently. VIGS was most effective in the seedling leaves 8 weeks after sowing, but was limited in duration and systemic spread. This study reports the first successful use of VIGS in Streptocarpus and in the family Gesneriaceae. The inoculation of viral sap derived from N. benthamiana was able to overcome the difficulties of standard Agrobacterium-mediated transformation in this genus. Irrespective of its transient effect, this VIGS system will be useful to assess gene function at the cellular level and represent an important tool for further understanding molecular mechanisms in Streptocarpus.
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Affiliation(s)
- Kanae Nishii
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, Scotland, UK.
- Kanagawa University, 2946, Tsuchiya, Hiratsuka-shi, Kanagawa, 259-1293, Japan.
| | - Yue Fei
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, Scotland, UK
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, Scotland, UK
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, Scotland, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, Scotland, UK.
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Courdavault V, Besseau S, Oudin A, Papon N, O'Connor SE. Virus-Induced Gene Silencing: Hush Genes to Make Them Talk. TRENDS IN PLANT SCIENCE 2020; 25:714-715. [PMID: 32526175 DOI: 10.1016/j.tplants.2020.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/21/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France.
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d'Angers, SFR 4208 ICAT, Angers, France
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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Liu M, Liang Z, Aranda MA, Hong N, Liu L, Kang B, Gu Q. A cucumber green mottle mosaic virus vector for virus-induced gene silencing in cucurbit plants. PLANT METHODS 2020; 16:9. [PMID: 32025236 PMCID: PMC6996188 DOI: 10.1186/s13007-020-0560-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/23/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cucurbits produce fruits or vegetables that have great dietary importance and economic significance worldwide. The published genomes of at least 11 cucurbit species are boosting gene mining and novel breeding strategies, however genetic transformation in cucurbits is impractical as a tool for gene function validation due to low transformation efficiency. Virus-induced gene silencing (VIGS) is a potential alternative tool. So far, very few ideal VIGS vectors are available for cucurbits. RESULTS Here, we describe a new VIGS vector derived from cucumber green mottle mosaic virus (CGMMV), a monopartite virus that infects cucurbits naturally. We show that the CGMMV vector is competent to induce efficient silencing of the phytoene desaturase (PDS) gene in the model plant Nicotiana benthamiana and in cucurbits, including watermelon, melon, cucumber and bottle gourd. Infection with the CGMMV vector harboring PDS sequences of 69-300 bp in length in the form of sense-oriented or hairpin cDNAs resulted in photobleaching phenotypes in N. benthamiana and cucurbits by PDS silencing. Additional results reflect that silencing of the PDS gene could persist for over two months and the silencing effect of CGMMV-based vectors could be passaged. CONCLUSIONS These results demonstrate that CGMMV vector could serve as a powerful and easy-to-use tool for characterizing gene function, controlling viral pathogens or even performing resistance breeding in cucurbits. Moreover, this study will possess considerable important reference value for developing different viral vectors.
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Affiliation(s)
- Mei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
- Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zhiling Liang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Miguel A. Aranda
- Centro de Edafologia y Biologia Aplicada del Segura (CEBAS)-CSIC, Apdo. Correos 164, Espinardo, 30100 Murcia, Spain
| | - Ni Hong
- Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Liming Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Baoshan Kang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
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Tavares-Esashika ML, Campos RNS, Blawid R, da Luz LL, Inoue-Nagata AK, Nagata T. Characterization of an infectious clone of pepper ringspot virus and its use as a viral vector. Arch Virol 2020; 165:367-375. [PMID: 31845151 DOI: 10.1007/s00705-019-04505-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/19/2019] [Indexed: 10/25/2022]
Abstract
The genus Tobravirus comprises three species: Tobacco rattle virus, Pea early-browning virus and Pepper ringspot virus. The genomes of tobraviruses consist of two positive-sense single-stranded RNA segments (RNA1 and RNA2). Infectious clones of TRV are extensively used as virus-induced gene-silencing (VIGS) vectors for studies of virus-host interactions and functions of plant genes. Complete infectious clones of pepper ringspot virus (PepRSV), the only tobravirus present in Brazil, however, have not yet been reported. Infectious clones will help to identify unique features of PepRSV RNA2 and provide another option for development of VIGS vectors. We constructed infectious clones based on two PepRSV isolates, CAM (RNA1 and RNA2) and LAV (RNA2). The cDNA constructs for both homologous (RNA1 and RNA2 of the CAM isolate) and heterologous (RNA1/CAM and RNA2/LAV) combinations were infectious in Nicotiana benthamiana plants. VIGS vector constructs with green fluorescent protein or phytoene desaturase genes inserted in RNA2 silenced the target genes. The systemic translocation of the PepRSV RNA1 construct alone (nonmultiple infection) was also confirmed in an N. benthamiana plant. These results are similar to those reported for tobacco rattle virus.
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Affiliation(s)
- Moana Lima Tavares-Esashika
- Campus Darcy Ribeiro, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Pós-graduação em Biologia Celular e Molecular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Ravi Narayan Souza Campos
- Campus Darcy Ribeiro, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Rosana Blawid
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, PE, 52171-900, Brazil
| | - Leonardo Lopes da Luz
- Pós-graduação em Biologia Microbiana, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | | | - Tatsuya Nagata
- Campus Darcy Ribeiro, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
- Pós-graduação em Biologia Celular e Molecular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
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Hong M, Chi ZH, Wang YQ, Tang YM, Deng QX, He MY, Wang RK, He YZ. Expression of a Chromoplast-Specific Lycopene β-Cyclase Gene ( CYC- B) Is Implicated in Carotenoid Accumulation and Coloration in the Loquat. Biomolecules 2019; 9:E874. [PMID: 31847172 PMCID: PMC6995616 DOI: 10.3390/biom9120874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 01/24/2023] Open
Abstract
Carotenoids are the principal pigments in the loquat. Although the metabolic pathway of plant carotenoids has been extensively investigated, few studies have been explored the regulatory mechanisms of loquat carotenoids because knowledge of the loquat genome is incomplete. The chromoplast-specific lycopene β-cyclase gene (CYC-B) could catalyze cyclization of lycopene to β-carotene. In this study, the differential accumulation patterns of loquat with different colors were analyzed and virus-induced gene silencing (VIGS) was utilized in order to verify CYC-B gene function. Using a cloning strategy of homologous genes, a CYC-B gene orthologue was successfully identified from the loquat. At a later stage of maturation, CYC-B gene expression and carotenoids concentrations in the 'Dawuxing' variety were higher than in 'Chuannong 1-5-9', possibly leading to the difference in pulp coloration of loquat. Interference of CYC-B gene expression in the loquat demonstrated clear visual changes. The green color in negative control fruits became yellow, while TRV2-CYC-B silenced fruits remained green. CYC-B gene expression and total carotenoid content in the pulp decreased by 32.5% and 44.1%, respectively. Furthermore, multiple key genes in the carotenoid metabolic pathway synergistically responded to downregulation of CYC-B gene expression. In summary, we provide direct evidences that CYC-B gene is involved in carotenoid accumulation and coloration in the loquat.
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Affiliation(s)
- Min Hong
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; (M.H.); (M.-Y.H.); (R.-K.W.); (Y.-Z.H.)
| | - Zhuo-Heng Chi
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Z.-H.C.); (Q.-X.D.)
| | - Yong-Qing Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Z.-H.C.); (Q.-X.D.)
| | - Yue-Ming Tang
- Institute of Agro-products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - Qun-Xian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Z.-H.C.); (Q.-X.D.)
| | - Ming-Yang He
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; (M.H.); (M.-Y.H.); (R.-K.W.); (Y.-Z.H.)
| | - Ri-Kui Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; (M.H.); (M.-Y.H.); (R.-K.W.); (Y.-Z.H.)
| | - Yi-Zhong He
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; (M.H.); (M.-Y.H.); (R.-K.W.); (Y.-Z.H.)
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Ortiz-Ramírez CI, Giraldo MA, Ferrándiz C, Pabón-Mora N. Expression and function of the bHLH genes ALCATRAZ and SPATULA in selected Solanaceae species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:686-702. [PMID: 31009131 DOI: 10.1111/tpj.14352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
The genetic mechanisms underlying fruit development have been identified in Arabidopsis and have been comparatively studied in tomato as a representative of fleshy fruits. However, comparative expression and functional analyses on the bHLH genes downstream the genetic network, ALCATRAZ (ALC) and SPATULA (SPT), which are involved in the formation of the dehiscence zone in Arabidopsis, have not been functionally studied in the Solanaceae. Here, we perform detailed expression and functional studies of ALC/SPT homologs in Nicotiana obtusifolia with capsules, and in Capsicum annuum and Solanum lycopersicum with berries. In Solanaceae, ALC and SPT genes are expressed in leaves, and all floral organs, especially in petal margins, stamens and carpels; however, their expression changes during fruit maturation according to the fruit type. Functional analyses show that downregulation of ALC/SPT genes does not have an effect on gynoecium patterning; however, they have acquired opposite roles in petal expansion and have been co-opted in leaf pigmentation in Solanaceae. In addition, ALC/SPT genes repress lignification in time and space during fruit development in Solanaceae. Altogether, some roles of ALC and SPT genes are different between Brassicaceae and Solanaceae; while the paralogs have undergone some subfunctionalization in the former they are mostly redundant in the latter.
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Affiliation(s)
- Clara Inés Ortiz-Ramírez
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Marco A Giraldo
- Instituto de Física, Universidad de Antioquia, Medellín, Colombia
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
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Xie L, Zhang Q, Sun D, Yang W, Hu J, Niu L, Zhang Y. Virus-induced gene silencing in the perennial woody Paeonia ostii. PeerJ 2019; 7:e7001. [PMID: 31179188 PMCID: PMC6545099 DOI: 10.7717/peerj.7001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/21/2019] [Indexed: 11/24/2022] Open
Abstract
Tree peony is a perennial deciduous shrub with great ornamental and medicinal value. A limitation of its current functional genomic research is the lack of effective molecular genetic tools. Here, the first application of a Tobacco rattle virus (TRV)-based virus-induced gene silencing (VIGS) in the tree peony species Paeonia ostii is presented. Two different approaches, leaf syringe-infiltration and seedling vacuum-infiltration, were utilized for Agrobacterium-mediated inoculation. The vacuum-infiltration was shown to result in a more complete Agrobacterium penetration than syringe-infiltration, and thereby determined as an appropriate inoculation method. The silencing of reporter gene PoPDS encoding phytoene desaturase was achieved in TRV-PoPDS-infected triennial tree peony plantlets, with a typical photobleaching phenotype shown in uppermost newly-sprouted leaves. The endogenous PoPDS transcripts were remarkably down-regulated in VIGS photobleached leaves. Moreover, the green fluorescent protein (GFP) fluorescence was detected in leaves and roots of plants inoculated with TRV-GFP, suggesting the capability of TRV to silence genes in various tissues. Taken together, the data demonstrated that the TRV-based VIGS technique could be adapted for high-throughput functional characterization of genes in tree peony.
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Affiliation(s)
- Lihang Xie
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingyu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Daoyang Sun
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Weizong Yang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayuan Hu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
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Hashimoto M, Yamaji Y, Komatsu K. Analysis of Antiviral Resistance Signaling Pathways by Virus-Induced Gene Silencing in Nicotiana benthamiana. Methods Mol Biol 2019; 2028:85-95. [PMID: 31228109 DOI: 10.1007/978-1-4939-9635-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Owing to the absence of antiviral chemicals, strategies to deploy antiviral resistance in plants are desirable. Deciphering antiviral resistance mechanisms has been extensively promoted by virus-induced gene silencing (VIGS) technique, which decreases the transcriptional level of the gene of interest via RNA silencing machinery triggered by the partial gene fragment inserted into a viral vector. This technique has contributed to addressing the function of a number of host genes, which are involved in signaling pathways leading to Resistance (R) protein-mediated resistance and the viral disease symptoms such as systemic necrosis. Here we describe the general VIGS protocol and its tips to analyze antiviral resistance mechanism using Tobacco rattle virus (TRV)-based VIGS vector in tobacco plant Nicotiana benthamiana. In most cases, the knockdown of host genes by TRV vector is highly efficient and uniform at the whole plant level but is not associated with any severe symptoms. Using this method together with inoculation of a challenge virus and transient overexpression of a viral elicitor or another host signaling component by agroinfiltration, as well as measurement of hallmarks of antiviral responses, we can address the role of the host factors and the epistatic relationship between several host factors in the resistance signaling pathway against plant virus infection. The protocol described here using the highly susceptible host N. benthamiana to a variety of plant viruses provides the opportunity to study resistance mechanisms underlying many host-virus interactions.
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Affiliation(s)
- Masayoshi Hashimoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan.
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Zhou J, Hunter DA, Lewis DH, McManus MT, Zhang H. Insights into carotenoid accumulation using VIGS to block different steps of carotenoid biosynthesis in petals of California poppy. PLANT CELL REPORTS 2018; 37:1311-1323. [PMID: 29922849 DOI: 10.1007/s00299-018-2314-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 05/08/2023]
Abstract
Viral-induced gene silencing of selected biosynthetic genes decreased overall carotenoid accumulation in California poppy. Regulation of carotenogenesis was linked with pigment sequestration, not changes in biosynthetic gene expression. Genes of carotenogenesis are well described, but understanding how they affect carotenoid accumulation has proven difficult because of plant lethality when the pigments are lacking. Here, we used a Tobacco Rattle Virus-based virus-induced-gene-silencing (VIGS) approach in California poppy (Eschscholzia californica) to investigate how silencing of the carotenoid biosynthetic pathway genes affects carotenoid metabolite accumulation and RNA transcript abundance of the carotenoid biosynthetic pathway genes. VIGS of upstream (PDS and ZDS) and downstream (βOH and ZEP) genes reduced transcript abundance of the targeted genes in the poppy petals while having no effect on abundance of the other carotenogenesis genes. Silencing of PDS, ZDS, βOH and ZEP genes reduced total pigment concentration by 75-90% and altered petal colour. HPLC and LC-MS measurements suggested that petal colour changes were caused by substantially altered pigment profiles and quantity. Carotenoid metabolites were different to those normally detected in wild-type petals accumulated but overall carotenoid concentration was less, suggesting the chemical form of carotenoid was important for whether it could be stored at high amounts. In poppy petals, eschscholtzxanthin and retro-carotene-triol were the predominant carotenoids, present mainly as esters. Specific esterification enzymes for specific carotenoids and/or fatty acids appear key for enabling petal carotenoids to accumulate to high amounts. Our findings argue against a direct role for carotenoid metabolites regulating carotenogenesis genes in the petals of California poppy as transcript abundance of carotenogenesis genes studied was unchanged, while the petal carotenoid metabolite profile changed substantially.
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Affiliation(s)
- Jun Zhou
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Donald A Hunter
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand.
| | - David H Lewis
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
| | - Michael T McManus
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Huaibi Zhang
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand.
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Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018; 19:1. [PMID: 29301551 PMCID: PMC5755456 DOI: 10.1186/s13059-017-1381-1] [Citation(s) in RCA: 391] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/13/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. CONCLUSIONS Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shouwei Ding
- Center for Plant Cell Biology, Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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Cheng C, Gao J, Ma N. Investigation of Petal Senescence by TRV-Mediated Virus-Induced Gene Silencing in Rose. Methods Mol Biol 2018; 1744:49-63. [PMID: 29392655 DOI: 10.1007/978-1-4939-7672-0_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The classic reverse genetic screening, such as EMS-induced or T-DNA-mediated mutation, is a powerful tool to identify senescence-related genes in many model plants. For most non-model plants, however, this strategy is hard to achieve. Even for model plants, construction of a mutant library is usually labor and time-consuming. Virus-induced gene silencing (VIGS) provides an alternative to characterize gene function in a wide spectrum of plants through transient gene expression. To date, more than a dozen of VIGS vector systems have been developed from different RNA and DNA viruses, while Tobacco rattle virus (TRV) system might be one of the most used due to its wide host range and ease of use. Here, we describe a modified TRV vector, TRV-GFP, in which a green fluorescent protein (GFP) is fused to 3'-end of the coat protein (CP) gene in the TRV2 vector. Since the GFP-tagged CP protein could be traced under UV light in planta, identification of TRV-GFP-infected plants is easy. Application of this system in identifying genes regulating petal senescence in rose is described.
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Affiliation(s)
- Chenxia Cheng
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, China Agricultural University, Beijing, China
| | - Junping Gao
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, China Agricultural University, Beijing, China
| | - Nan Ma
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China. .,Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, China Agricultural University, Beijing, China.
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44
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Kant R, Dasgupta I. Phenotyping of VIGS-mediated gene silencing in rice using a vector derived from a DNA virus. PLANT CELL REPORTS 2017; 36:1159-1170. [PMID: 28540496 DOI: 10.1007/s00299-017-2156-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/15/2017] [Indexed: 05/09/2023]
Abstract
Target genes in rice can be optimally silenced if inserted in antisense or hairpin orientation in the RTBV-derived VIGS vector and plants grown at 28 °C and 80% humidity after inoculation. Virus induced gene silencing (VIGS) is a method used to transiently silence genes in dicot as well as monocot plants. For the important monocot species rice, the Rice tungro bacilliform virus (RTBV)-derived VIGS system (RTBV-VIGS), which uses agroinoculation to initiate silencing, has not been standardized for optimal use. Here, using RTBV-VIGS, three sets of conditions were tested to achieve optimal silencing of the rice marker gene phytoene desaturase (pds). The effect of orientation of the insert in the RTBV-VIGS plasmid (sense, antisense and hairpin) on the silencing of the target gene was then evaluated using rice magnesium chelatase subunit H (chlH). Finally, the rice Xa21 gene, conferring resistance against bacterial leaf blight disease (BLB) was silenced using RTBV-VIGS system. In each case, real-time PCR-based assessment indicated approximately 40-80% fall in the accumulation levels of the transcripts of pds, chlH and Xa21. In the case of pds, the appearance of white streaks in the emerging leaves, and for chlH, chlorophyll levels and F v/F m ratio were assessed as phenotypes for silencing. For Xa21, the resistance levels to BLB were assessed by measuring the lesion length and the percent diseased areas of leaves, following challenge inoculation with Xanthomonas oryzae. In each case, the RTBV-MVIGS system gave rise to a discernible phenotype indicating the silencing of the respective target gene using condition III (temperature 28 °C, humidity 80% and 1 mM MES and 20 µM acetosyringone in secondary agrobacterium culture), which revealed the robustness of this gene silencing system for rice.
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Affiliation(s)
- Ravi Kant
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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45
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Tran PT, Choi H, Choi D, Kim KH. Virus-induced gene silencing reveals signal transduction components required for the Pvr9-mediated hypersensitive response in Nicotiana benthamiana. Virology 2016; 495:167-72. [PMID: 27236305 DOI: 10.1016/j.virol.2016.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/12/2016] [Accepted: 05/15/2016] [Indexed: 01/03/2023]
Abstract
Resistance to pathogens mediated by plant resistance (R) proteins requires different signaling transduction components and pathways. Our previous studies revealed that a potyvirus resistance gene in pepper, Pvr9, confers a hypersensitive response (HR) to pepper mottle virus in Nicotiana benthamiana. Our results show that the Pvr9-mediated HR against pepper mottle virus infection requires HSP90, SGT1, NDR1, but not EDS1. These results suggest that the Pvr9-mediated HR is possibly related to the SA pathway but not the ET, JA, ROS or NO pathways.
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Affiliation(s)
- Phu-Tri Tran
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Doil Choi
- Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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46
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Preston JC, Jorgensen SA, Orozco R, Hileman LC. Paralogous SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes differentially regulate leaf initiation and reproductive phase change in petunia. PLANTA 2016; 243:429-40. [PMID: 26445769 PMCID: PMC4722060 DOI: 10.1007/s00425-015-2413-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/22/2015] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Duplicated petunia clade-VI SPL genes differentially promote the timing of inflorescence and flower development, and leaf initiation rate. The timing of plant reproduction relative to favorable environmental conditions is a critical component of plant fitness, and is often associated with variation in plant architecture and habit. Recent studies have shown that overexpression of the microRNA miR156 in distantly related annual species results in plants with perennial characteristics, including late flowering, weak apical dominance, and abundant leaf production. These phenotypes are largely mediated through the negative regulation of a subset of genes belonging to the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors. In order to determine how and to what extent paralogous SPL genes have partitioned their roles in plant growth and development, we functionally characterized petunia clade-VI SPL genes under different environmental conditions. Our results demonstrate that PhSBP1and PhSBP2 differentially promote discrete stages of the reproductive transition, and that PhSBP1, and possibly PhCNR, accelerates leaf initiation rate. In contrast to the closest homologs in annual Arabidopsis thaliana and Mimulus guttatus, PhSBP1 and PhSBP2 transcription is not mediated by the gibberellic acid pathway, but is positively correlated with photoperiod and developmental age. The developmental functions of clade-VI SPL genes have, thus, evolved following both gene duplication and speciation within the core eudicots, likely through differential regulation and incomplete sub-functionalization.
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Affiliation(s)
- Jill C Preston
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA.
| | - Stacy A Jorgensen
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Rebecca Orozco
- Ecology and Evolutionary Biology, The University of Kansas, 8009 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Lena C Hileman
- Ecology and Evolutionary Biology, The University of Kansas, 8009 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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Chantreau M, Chabbert B, Billiard S, Hawkins S, Neutelings G. Functional analyses of cellulose synthase genes in flax (Linum usitatissimum) by virus-induced gene silencing. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:1312-24. [PMID: 25688574 DOI: 10.1111/pbi.12350] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 01/05/2015] [Accepted: 01/08/2015] [Indexed: 05/08/2023]
Abstract
Flax (Linum usitatissimum) bast fibres are located in the stem cortex where they play an important role in mechanical support. They contain high amounts of cellulose and so are used for linen textiles and in the composite industry. In this study, we screened the annotated flax genome and identified 14 distinct cellulose synthase (CESA) genes using orthologous sequences previously identified. Transcriptomics of 'primary cell wall' and 'secondary cell wall' flax CESA genes showed that some were preferentially expressed in different organs and stem tissues providing clues as to their biological role(s) in planta. The development for the first time in flax of a virus-induced gene silencing (VIGS) approach was used to functionally evaluate the biological role of different CESA genes in stem tissues. Quantification of transcript accumulation showed that in many cases, silencing not only affected targeted CESA clades, but also had an impact on other CESA genes. Whatever the targeted clade, inactivation by VIGS affected plant growth. In contrast, only clade 1- and clade 6-targeted plants showed modifications in outer-stem tissue organization and secondary cell wall formation. In these plants, bast fibre number and structure were severely impacted, suggesting that the targeted genes may play an important role in the establishment of the fibre cell wall. Our results provide new fundamental information about cellulose biosynthesis in flax that should facilitate future plant improvement/engineering.
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Affiliation(s)
- Maxime Chantreau
- UMR INRA 1281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Université Lille Nord de France Lille 1, Villeneuve d'Ascq, France
| | - Brigitte Chabbert
- INRA, UMR 614 Fractionnement des AgroRessources et Environnement, Reims, France
- UMR 614 Fractionnement des AgroRessources et Environnement, Université de Reims Champagne-Ardenne, Reims, France
| | - Sylvain Billiard
- UMR CNRS 8198 Laboratoire de Génétique & Evolution des Populations Végétales, Université Lille Nord de France Lille 1, Villeneuve d'Ascq, France
| | - Simon Hawkins
- UMR INRA 1281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Université Lille Nord de France Lille 1, Villeneuve d'Ascq, France
| | - Godfrey Neutelings
- UMR INRA 1281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Université Lille Nord de France Lille 1, Villeneuve d'Ascq, France
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48
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Schaeffer SM, Nakata PA. CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:130-42. [PMID: 26475194 DOI: 10.1016/j.plantsci.2015.09.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 05/22/2023]
Abstract
The CRISPR/Cas9 genome engineering system has ignited and swept through the scientific community like wildfire. Owing largely to its efficiency, specificity, and flexibility, the CRISPR/Cas9 system has quickly become the preferred genome-editing tool of plant scientists. In plants, much of the early CRISPR/Cas9 work has been limited to proof of concept and functional studies in model systems. These studies, along with those in other fields of biology, have led to the development of several utilities of CRISPR/Cas9 beyond single gene editing. Such utilities include multiplexing for inducing multiple cleavage events, controlling gene expression, and site specific transgene insertion. With much of the conceptual CRISPR/Cas9 work nearly complete, plant researchers are beginning to apply this gene editing technology for crop trait improvement. Before rational strategies can be designed to implement this technology to engineer a wide array of crops there is a need to expand the availability of crop-specific vectors, genome resources, and transformation protocols. We anticipate that these challenges will be met along with the continued evolution of the CRISPR/Cas9 system particularly in the areas of manipulation of large genomic regions, transgene-free genetic modification, development of breeding resources, discovery of gene function, and improvements upon CRISPR/Cas9 components. The CRISPR/Cas9 editing system appears poised to transform crop trait improvement.
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Affiliation(s)
- Scott M Schaeffer
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030-2600, United States
| | - Paul A Nakata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030-2600, United States.
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49
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Fernandez-Pozo N, Rosli HG, Martin GB, Mueller LA. The SGN VIGS tool: user-friendly software to design virus-induced gene silencing (VIGS) constructs for functional genomics. MOLECULAR PLANT 2015; 8:486-8. [PMID: 25667001 DOI: 10.1016/j.molp.2014.11.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/21/2014] [Accepted: 11/30/2014] [Indexed: 05/13/2023]
Affiliation(s)
| | - Hernan G Rosli
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús (IIB-INTECH), UNSAM-CONICET, Chascomús, B7130IWA Buenos Aires, Argentina
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
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50
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Goodin MM, Zaitlin D, Naidu RA, Lommel SA. Nicotiana benthamiana: Its History and Future as a Model for Plant-Pathogen Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:28-39. [PMID: 27839076 DOI: 10.1094/mpmi-00-00-1015-rev.testissue] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nicotiana benthamiana is the most widely used experimental host in plant virology, due mainly to the large number of diverse plant viruses that can successfully infect it. Addi- tionally, N. benthamiana is susceptible to a wide variety of other plant-pathogenic agents (such as bacteria, oomycetes, fungi, and so on), making this species a cornerstone of host-pathogen research, particularly in the context of innate immunity and defense signaling. Moreover, because it can be genetically transformed and regenerated with good efficiency and is amenable to facile methods for virus- induced gene silencing or transient protein expression, N. benthamiana is rapidly gaining popularity in plant biology, particularly in studies requiring protein localization, inter- action, or plant-based systems for protein expression and purification. Paradoxically, despite being an indispensable research model, little is known about the origins, genetic variation, or ecology of the N. benthamiana accessions cur- rently used by the research community. In addition to ad- dressing these latter topics, the purpose of this review is to provide information regarding sources for tools and reagents that can be used to support research in N. benthamiana. Finally, we propose that N. benthamiana is well situated to become a premier plant cell biology model, particularly for the virology community, who as a group were the first to recognize the potential of this unique Australian native.
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Affiliation(s)
| | - David Zaitlin
- 2 Kentucky Tobacco Research and Development Center (KTRDC), University of Kentucky, Lexington 40546, U.S.A
| | - Rayapati A Naidu
- 3 Department of Plant Pathology, Irrigated Agriculture Research & Extension Center, Washington State University, Prosser 99350, U.S.A
| | - Steven A Lommel
- 4 Department of Plant Pathology, North Carolina State University, Raleigh 27695, U.S.A
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