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Shahwar D, Ahn N, Kim D, Ahn W, Park Y. Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108473. [PMID: 37716439 DOI: 10.1016/j.mrrev.2023.108473] [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: 03/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023]
Abstract
Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Namju Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Donghyun Kim
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Wooseong Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea.
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2
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Ajmal M, Hussain A, Ali A, Chen H, Lin H. Strategies for Controlling the Sporulation in Fusarium spp. J Fungi (Basel) 2022; 9:jof9010010. [PMID: 36675831 PMCID: PMC9861637 DOI: 10.3390/jof9010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Fusarium species are the most destructive phytopathogenic and toxin-producing fungi, causing serious diseases in almost all economically important plants. Sporulation is an essential part of the life cycle of Fusarium. Fusarium most frequently produces three different types of asexual spores, i.e., macroconidia, chlamydospores, and microconidia. It also produces meiotic spores, but fewer than 20% of Fusaria have a known sexual cycle. Therefore, the asexual spores of the Fusarium species play an important role in their propagation and infection. This review places special emphasis on current developments in artificial anti-sporulation techniques as well as features of Fusarium's asexual sporulation regulation, such as temperature, light, pH, host tissue, and nutrients. This description of sporulation regulation aspects and artificial anti-sporulation strategies will help to shed light on the ways to effectively control Fusarium diseases by inhibiting the production of spores, which eventually improves the production of food plants.
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Affiliation(s)
- Maria Ajmal
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Adil Hussain
- Department of Entomology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Asad Ali
- Department of Entomology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Hui Lin
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
- Correspondence:
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3
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Zhang H, Demirer GS, Zhang H, Ye T, Goh NS, Aditham AJ, Cunningham FJ, Fan C, Landry MP. DNA nanostructures coordinate gene silencing in mature plants. Proc Natl Acad Sci U S A 2019; 116:7543-7548. [PMID: 30910954 PMCID: PMC6462094 DOI: 10.1073/pnas.1818290116] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Delivery of biomolecules to plants relies on Agrobacterium infection or biolistic particle delivery, the former of which is amenable only to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall, which is absent in mammalian cells and poses the dominant physical barrier to biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells; however, nanoparticle-mediated delivery without external mechanical aid remains unexplored for biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver siRNAs, and effectively silence a constitutively expressed gene in Nicotiana benthamiana leaves. We show that nanostructure internalization into plant cells and corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures and both details the design parameters of importance for plant cell internalization and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.
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Affiliation(s)
- Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Honglu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Tianzheng Ye
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Abhishek J Aditham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Chinese Academy of Sciences Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720;
- Innovative Genomics Institute, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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4
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Laha T, Brindley PJ, Suyapoh W, Suttiprapa S. RNA Interference as an Approach to Functional Genomics Genetic Manipulation of Opisthorchis viverrini. ADVANCES IN PARASITOLOGY 2018; 102:25-43. [PMID: 30442309 DOI: 10.1016/bs.apar.2018.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The availability of genome and transcriptome data of the liver fluke Opisthorchis viverrini provides the foundation for exploration of gene function and its effect on host-parasite interactions and pathogenesis of O. viverrini-associated bile duct cancer. Functional genomics approaches address the function of DNA at levels of the gene, RNA transcript and protein product using informative manipulations of the genome, epigenome, transcriptome, proteome, microbiome and metabolome. Advances in functional genomics for O. viverrini have thus far focused on RNA interference. The flukes have been transfected with double-stranded RNAs aiming to silence target gene expression. In general, this approach for functional genomics investigation of this pathogen has been found to be tractable and efficient: suppression of messenger RNA expression in O. viverrini results in reduction of protein activity and phenotypic changes. Future perspectives for functional genomics of this liver fluke and close phylogenetic relatives are also discussed.
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Affiliation(s)
- Thewarach Laha
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Paul J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Tropical Diseases of Poverty, School of Medicine & Health Sciences, The George Washington University, Washington DC, United States
| | - Watcharapol Suyapoh
- Biomedical Science Graduate Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand
| | - Sutas Suttiprapa
- Tropical Disease Research Center, Tropical Medicine Graduate Program, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Nakamura S, Uehara H, Hasegawa T, Fujimoto K. Phototriggered Sequence-specific DNA Transportation into Liposomes Using Ultrafast DNA Photocrosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.170835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Harunobu Uehara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Takashi Hasegawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
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Zhang J, Yu D, Zhang Y, Liu K, Xu K, Zhang F, Wang J, Tan G, Nie X, Ji Q, Zhao L, Li C. Vacuum and Co-cultivation Agroinfiltration of (Germinated) Seeds Results in Tobacco Rattle Virus (TRV) Mediated Whole-Plant Virus-Induced Gene Silencing (VIGS) in Wheat and Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:393. [PMID: 28382049 PMCID: PMC5360694 DOI: 10.3389/fpls.2017.00393] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/07/2017] [Indexed: 05/06/2023]
Abstract
Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) has been frequently used in dicots. Here we show that it can also be used in monocots, by presenting a system involving use of a novel infiltration solution (containing acetosyringone, cysteine, and Tween 20) that enables whole-plant level VIGS of (germinated) seeds in wheat and maize. Using the established system, phytoene desaturase (PDS) genes were successfully silenced, resulting in typical photo-bleaching symptoms in the leaves of treated wheat and maize. In addition, three wheat homoeoalleles of MLO, a key gene repressing defense responses to powdery mildew in wheat, were simultaneously silenced in susceptible wheat with this system, resulting in it becoming resistant to powdery mildew. The system has the advantages generally associated with TRV-mediated VIGS systems (e.g., high-efficiency, mild virus infection symptoms, and effectiveness in different organs). However, it also has the following further advantages: (germinated) seed-stage agroinfiltration; greater rapidity and convenience; whole-plant level gene silencing; adequately stable transformation; and suitability for studying functions of genes involved in seed germination and early plant development stages.
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Affiliation(s)
- Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Deshui Yu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Yi Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Kun Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Xianhui Nie
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Qiaohua Ji
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Lu Zhao
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Chengwei Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Technology, Henan Institute of Science and Technology, XinxiangChina
- *Correspondence: Chengwei Li,
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Shi X, Zhang X, Chang Y, Jiang B, Deng R, Wang A, Zhang G. Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells. BMC Vet Res 2016; 12:90. [PMID: 27268206 PMCID: PMC4895886 DOI: 10.1186/s12917-016-0717-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/01/2016] [Indexed: 01/06/2023] Open
Abstract
Background Porcine reproductive and respiratory syndrome virus (PRRSV) induces one of most important devastating disease of swine worldwide, and the current methods poorly control it. Previous studies have indicated that the nonstructural protein 11 (nsp11) of PRRSV may be an important protein for the immune escape of PRRSV. Results Here, we firstly explored the effect of over-expression of nsp11 on PRRSV infection and found that over-expression of nsp11 enhanced the PRRSV titers while the small interfering RNA (siRNAs) specifically targeting nsp11 could reduce the PRRSV titers in MARC-145 cells. Conclusion In conclusion, PRRSV nsp11 promotes PRRSV infection in MARC-145 cells and siRNAs targeting nsp11 may be a potential therapeutic strategy to control PRRSV in future.
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Affiliation(s)
- Xibao Shi
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China. .,Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
| | - Xiaozhuan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Yongzhe Chang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Bo Jiang
- Office of Science & Technology, Chongqing Police College, Chongqing, 401331, China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Aiping Wang
- Department of Bioengineering, Zhengzhou University, Zhengzhou, Henan, 450000, 450002, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China. .,College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
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Bhandare VV, Ramaswamy A. Identification of possible siRNA molecules for TDP43 mutants causing amyotrophic lateral sclerosis: In silico design and molecular dynamics study. Comput Biol Chem 2016; 61:97-108. [PMID: 26854610 DOI: 10.1016/j.compbiolchem.2016.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 12/29/2015] [Accepted: 01/08/2016] [Indexed: 12/12/2022]
Abstract
The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a systematic theoretical approach including (i) identification of respective codons for all mutants (reported at the protein level) based on both minimum free energy and probabilistic approaches, (ii) rational design of siRNA, (iii) secondary structure analysis for the target accessibility of siRNA, (iii) determination of the ability of siRNA to interact with mRNA and the formation/stability of duplex via molecular dynamics study for a period of 15ns and (iv) characterization of mRNA-siRNA duplex stability based on thermo-physical analysis. The stable GC-rich siRNA expressed strong binding affinity towards mRNA and forms stable duplex in A-form. The linear dependence between the thermo-physical parameters such as Tm, GC content and binding free energy revealed the ability of the identified siRNAs to interact with mRNA in comparable to that of the experimentally reported siRNAs. Hence, this present study proposes few siRNAs as the possible gene silencing agents in RNAi therapy based on the in silico approach.
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Affiliation(s)
| | - Amutha Ramaswamy
- Centre for Bioinformatics, Pondicherry University, Pondicherry 605014, India.
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9
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A long downstream probe-based platform for multiplex target capture. Anal Biochem 2015; 491:4-9. [PMID: 26344895 DOI: 10.1016/j.ab.2015.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 11/20/2022]
Abstract
A simple and rapid detection platform was established for multiplex target capture through generating single-strand long downstream probe (ssLDP), which was integrated with the ligase detection reaction (LDR) method for the purpose of multiplicity and high specificity. To increase sensitivity, the ladder-like polymerase chain reaction (PCR) amplicons were generated by using universal primers that complement ligated products. Each of the amplicons contained a stuffer sequence with a defined yet variable length. Thus, the length of the amplicon is an index of the specific suppressor, allowing its identification via electrophoresis. The multiplexed diagnostic platform was optimized using standard plasmids and validated by using potato virus suppressors as a detection model. This technique can detect down to 1.2 × 10(3) copies for single or two mixed target plasmids. When compared with microarray results, the electrophoresis showed 98.73-100% concordance rates for the seven suppressors in the 79 field samples. This strategy could be applied to detect a large number of targets in field and clinical surveillance.
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10
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RNAi: antiviral therapy against dengue virus. Asian Pac J Trop Biomed 2015; 3:232-6. [PMID: 23620845 DOI: 10.1016/s2221-1691(13)60057-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 02/25/2013] [Indexed: 01/01/2023] Open
Abstract
Dengue virus infection has become a global threat affecting around 100 countries in the world. Currently, there is no licensed antiviral agent available against dengue. Thus, there is a strong need to develop therapeutic strategies that can tackle this life threatening disease. RNA interference is an important and effective gene silencing process which degrades targeted RNA by a sequence specific process. Several studies have been conducted during the last decade to evaluate the efficiency of siRNA in inhibiting dengue virus replication. This review summarizes siRNAs as a therapeutic approach against dengue virus serotypes and concludes that siRNAs against virus and host genes can be next generation treatment of dengue virus infection.
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Shi X, Chang Y, Zhang X, Wang L, Li C, Jiang K, Chen J, Wang C, Deng R, Fan J, Zhang G. Small interfering RNA targeting nonstructural protein1 α (nsp1α) of porcine reproductive and respiratory syndrome virus (PRRSV) can reduce the replication of PRRSV in MARC-145 cells. Res Vet Sci 2015; 99:215-7. [PMID: 25683113 PMCID: PMC7111734 DOI: 10.1016/j.rvsc.2015.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 11/15/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically devastating and pandemic diseases of swine, which is poorly controlled by current methods. The inhibition of specific genes by small interfering RNA (siRNA) has been proven to be a potential therapeutic strategy against viral infection. Previous studies have indicated that the nonstructural protein 1α (nsp1α) of PRRSV may take an important role in virulence of PRRSV. The present work was involved to explore the effect of siRNA targeting nsp1α on the replication of PRRSV in MARC-145 cells, and the results showed that over-expression of nsp1α enhanced the replication of PRRSV and that siRNAs specifically targeting nsp1α significantly inhibited the replication of PRRSV in MARC-145 cells. In conclusion, this work indicated that nsp1α may be a viral pathogenicity factor of PRRSV and that siRNAs specifically targeting nsp1α may be a new strategy to control PRRSV in the future.
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Affiliation(s)
- Xibao Shi
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Yongzhe Chang
- College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Xiaozhuan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; College of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Li Wang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Chunxi Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Kai Jiang
- College of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Jing Chen
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Chao Wang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Jianming Fan
- The Laboratory of Toxicology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Gaiping Zhang
- College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China.
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12
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Hu Z, Parekh U, Maruta N, Trusov Y, Botella JR. Down-regulation of Fusarium oxysporum endogenous genes by Host-Delivered RNA interference enhances disease resistance. Front Chem 2015; 3:1. [PMID: 25654075 PMCID: PMC4299518 DOI: 10.3389/fchem.2015.00001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/01/2015] [Indexed: 01/17/2023] Open
Abstract
Fusarium oxysporum is a devastating pathogen causing extensive yield losses in a variety of crops and development of sustainable, environmentally friendly methods to improve crop resistance is crucial. We have used Host-Delivered RNA interference (HD-RNAi) technology to partially silence three different genes (FOW2, FRP1, and OPR) in the hemi-biotrophic fungus F. oxysporum f. sp. conglutinans. Expression of double stranded RNA (dsRNA) molecules targeting fungal pathogen genes was achieved in a number of transgenic Arabidopsis lines. F. oxysporum infecting the transgenic lines displayed substantially reduced mRNA levels on all three targeted genes, with an average of 75, 83, and 72% reduction for FOW2, FRP1, and OPR, respectively. The silencing of pathogen genes had a clear positive effect on the ability of the transgenic lines to fight infection. All transgenic lines displayed enhanced resistance to F. oxysporum with delayed disease symptom development, especially FRP1 and OPR lines. Survival rates after fungal infection were higher in the transgenic lines compared to control wild type plants which consistently showed survival rates of 10%, with FOW2 lines showing 25% survival; FRP1 lines 30-50% survival and OPR between 45 and 70% survival. The down-regulation effect was specific for the targeted genes without unintended effects in related genes. In addition to producing resistant crops, HD-RNAi can provide a useful tool to rapidly screen candidate fungal pathogenicity genes without the need to produce fungal knockout mutants.
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Affiliation(s)
- Zongli Hu
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
- Bioengineering College, Chongqing UniversityChongqing, China
| | - Urvi Parekh
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Natsumi Maruta
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Yuri Trusov
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Jose R. Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
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13
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Jiang L, Ding L, He B, Shen J, Xu Z, Yin M, Zhang X. Systemic gene silencing in plants triggered by fluorescent nanoparticle-delivered double-stranded RNA. NANOSCALE 2014; 6:9965-9. [PMID: 25068243 DOI: 10.1039/c4nr03481c] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A cationic fluorescence nanoparticle efficiently enters plants with high transfection efficacy. Applying a mixture of G2/dsRNA to the model plant, Arabidopsis root, leads to significant reduction in the expression of important developmental genes and results in apparent phenotypes. This study reports a non-viral gene nanocarrier which triggers gene silencing in plants and leads to systemic phenotypes.
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Affiliation(s)
- Li Jiang
- College of Agronomy and Biotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
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Hayata K, Asada S, Fujii T, Inoue H, Ishikawa K, Sawayama S. Gene targeting by RNAi-mediated knockdown of potent DNA ligase IV homologue in the cellulase-producing fungus Talaromyces cellulolyticus. Appl Biochem Biotechnol 2014; 174:1697-704. [PMID: 25161035 DOI: 10.1007/s12010-014-1142-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/04/2014] [Indexed: 01/12/2023]
Abstract
The genome of the cellulase-producing fungus Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) was screened for a potent DNA ligase IV gene (ligD homologue). Homologous recombination efficiency in T. cellulolyticus is very low. Therefore, suppression of a non-homologous end-joining system was attempted to enable specific gene knockouts for molecular breeding. The transcript levels of ligD homologue were 0.037 of those of the parental YP-4 strain in the Li20 transformant carrying the RNAi construct targeting the ligD homologue. Transformation of the hairpin-type RNAi vector into T. cellulolyticus could be useful in fungal gene knockdown experiments. Cellulase production and protein secretion were similar in the parental YP-4 strain and the Li20 transformant. Knockout transformation of ligD homologue using the Li20 transformant led to 23.1 % double crossover gene targeting. Our results suggest that the potent DNA ligase IV gene of T. cellulolyticus is related to non-homologous end joining and that the knockdown of the ligD homologue is useful in gene targeting.
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Affiliation(s)
- Koutarou Hayata
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
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15
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Kang Z, Zhang C, Zhang J, Jin P, Zhang J, Du G, Chen J. Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3413-24. [DOI: 10.1007/s00253-014-5569-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/17/2022]
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16
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Posiri P, Ongvarrasopone C, Panyim S. A simple one-step method for producing dsRNA from E. coli to inhibit shrimp virus replication. J Virol Methods 2013; 188:64-9. [DOI: 10.1016/j.jviromet.2012.11.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 11/17/2012] [Accepted: 11/21/2012] [Indexed: 12/28/2022]
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17
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Alberg AJ, Jorgensen TJ, Ruczinski I, Wheless L, Shugart YY, Berthier-Schaad Y, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao WHL, Francis L, Alani RM, Smith MW, Strickland PT. DNA repair gene variants in relation to overall cancer risk: a population-based study. Carcinogenesis 2012; 34:86-92. [PMID: 23027618 DOI: 10.1093/carcin/bgs304] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The hypothesis that germ-line polymorphisms in DNA repair genes influence cancer risk has previously been tested primarily on a cancer site-specific basis. The purpose of this study was to test the hypothesis that DNA repair gene allelic variants contribute to globally elevated cancer risk by measuring associations with risk of all cancers that occurred within a population-based cohort. In the CLUE II cohort study established in 1989 in Washington County, MD, this study was comprised of all 3619 cancer cases ascertained through 2007 compared with a sample of 2296 with no cancer. Associations were measured between 759 DNA repair gene single nucleotide polymorphisms (SNPs) and risk of all cancers. A SNP in O(6)-methylguanine-DNA methyltransferase, MGMT, (rs2296675) was significantly associated with overall cancer risk [per minor allele odds ratio (OR) 1.30, 95% confidence interval (CI) 1.19-1.43 and P-value: 4.1 × 10(-8)]. The association between rs2296675 and cancer risk was stronger among those aged ≤54 years old than those who were ≥55 years at baseline (P-for-(interaction) = 0.021). OR were in the direction of increased risk for all 15 categories of malignancies studied (P < 0.0001), ranging from 1.22 (P = 0.42) for ovarian cancer to 2.01 (P = 0.008) for urinary tract cancers; the smallest P-value was for breast cancer (OR 1.45, P = 0.0002). The results indicate that the minor allele of MGMT SNP rs2296675, a common genetic marker with 37% carriers, was significantly associated with increased risk of cancer across multiple tissues. Replication is needed to more definitively determine the scientific and public health significance of this observed association.
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Affiliation(s)
- Anthony J Alberg
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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18
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Role of RNA interference in plant improvement. Naturwissenschaften 2011; 98:473-92. [PMID: 21503773 DOI: 10.1007/s00114-011-0798-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/06/2011] [Accepted: 04/08/2011] [Indexed: 01/07/2023]
Abstract
Research to alter crops for their better performance involving modern technology is underway in numerous plants, and achievements in transgenic plants are impacting crop improvements in unparalleled ways. Striking progress has been made using genetic engineering technology over the past two decades in manipulating genes from diverse and exotic sources, and inserting them into crop plants for inducing desirable characteristics. RNA interference (RNAi) has recently been identified as a natural mechanism for regulation of gene expression in all higher organisms from plants to humans and promises greater accuracy and precision to plant improvement. The expression of any gene can be down-regulated in a highly explicit manner exclusive of affecting the expression of any other gene by using RNAi technologies. Additional research in this field has been focused on a number of other areas including microRNAs, hairpin RNA, and promoter methylation. Manipulating new RNAi pathways, which generate small RNA molecules to amend gene expression in crops, can produce new quality traits and having better potentiality of protection against abiotic and biotic stresses. Nutritional improvement, change in morphology, or enhanced secondary metabolite synthesis are some of the other advantages of RNAi technology. In addition to its roles in regulating gene expression, RNAi is also used as a natural defense mechanism against molecular parasites such as jumping genes and viral genetic elements that affect genome stability. Even though much advancement has been made on the field of RNAi over the preceding few years, the full prospective of RNAi for crop improvement remains to be fully realized. The intricacy of RNAi pathway, the molecular machineries, and how it relates to plant development are still to be explained.
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Pérez-Quintero ÁL, Neme R, Zapata A, López C. Plant microRNAs and their role in defense against viruses: a bioinformatics approach. BMC PLANT BIOLOGY 2010; 10:138. [PMID: 20594353 PMCID: PMC3017820 DOI: 10.1186/1471-2229-10-138] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 07/01/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are non-coding short RNAs that regulate gene expression in eukaryotes by translational inhibition or cleavage of complementary mRNAs. In plants, miRNAs are known to target mostly transcription factors and are implicated in diverse aspects of plant growth and development. A role has been suggested for the miRNA pathway in antiviral defense in plants. In this work, a bioinformatics approach was taken to test whether plant miRNAs from six species could have antiviral activity by targeting the genomes of plant infecting viruses. RESULTS All plants showed a repertoire of miRNAs with potential for targeting viral genomes. The viruses were targeted by abundant and conserved miRNA families in regions coding for cylindrical inclusion proteins, capsid proteins, and nuclear inclusion body proteins. The parameters for our predicted miRNA:target pairings in the viral genomes were similar to those for validated targets in the plant genomes, indicating that our predicted pairings might behave in-vivo as natural miRNa-target pairings. Our screening was compared with negative controls comprising randomly generated miRNAs, animal miRNAs, and genomes of animal-infecting viruses. We found that plant miRNAs target plant viruses more efficiently than any other sequences, but also, miRNAs can either preferentially target plant-infecting viruses or target any virus without preference. CONCLUSIONS Our results show a strong potential for antiviral activity of plant miRNAs and suggest that the miRNA pathway may be a support mechanism to the siRNA pathway in antiviral defense.
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Affiliation(s)
- Álvaro L Pérez-Quintero
- Universidad Nacional de Colombia, Bogotá, Departamento de Biología, Oficina 222. Calle 45 Cra 30. Bogota D.C. Colombia
| | - Rafik Neme
- Universidad Nacional de Colombia, Bogotá, Departamento de Biología, Oficina 222. Calle 45 Cra 30. Bogota D.C. Colombia
| | - Andrés Zapata
- Universidad Nacional de Colombia, Bogotá, Departamento de Biología, Oficina 222. Calle 45 Cra 30. Bogota D.C. Colombia
| | - Camilo López
- Universidad Nacional de Colombia, Bogotá, Departamento de Biología, Oficina 222. Calle 45 Cra 30. Bogota D.C. Colombia
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Dielen AS, Badaoui S, Candresse T, German-Retana S. The ubiquitin/26S proteasome system in plant-pathogen interactions: a never-ending hide-and-seek game. MOLECULAR PLANT PATHOLOGY 2010; 11:293-308. [PMID: 20447278 PMCID: PMC6640532 DOI: 10.1111/j.1364-3703.2009.00596.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ubiquitin/26S proteasome system (UPS) plays a central role in plant protein degradation. Over the past few years, the importance of this pathway in plant-pathogen interactions has been increasingly highlighted. UPS is involved in almost every step of the defence mechanisms in plants, regardless of the type of pathogen. In addition to its proteolytic activities, UPS, through its 20S RNase activity, may be part of a still unknown antiviral defence pathway. Strikingly, UPS is not only a weapon used by plants to defend themselves, but also a target for some pathogens that have evolved mechanisms to inhibit and/or use this system for their own purposes. This article attempts to summarize the current knowledge on UPS involvement in plant-microbe interactions, a complex scheme that illustrates the never-ending arms race between hosts and microbes.
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Affiliation(s)
- Anne-Sophie Dielen
- Interactions Plante-Virus, UMR GDPP 1090, INRA Université de Bordeaux 2, BP 81, F-33883 Villenave d'Ornon Cedex, France
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21
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Solis CF, Santi-Rocca J, Perdomo D, Weber C, Guillén N. Use of bacterially expressed dsRNA to downregulate Entamoeba histolytica gene expression. PLoS One 2009; 4:e8424. [PMID: 20037645 PMCID: PMC2793006 DOI: 10.1371/journal.pone.0008424] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 11/24/2009] [Indexed: 11/18/2022] Open
Abstract
Background Modern RNA interference (RNAi) methodologies using small interfering RNA (siRNA) oligonucleotide duplexes or episomally synthesized hairpin RNA are valuable tools for the analysis of gene function in the protozoan parasite Entamoeba histolytica. However, these approaches still require time-consuming procedures including transfection and drug selection, or costly synthetic molecules. Principal Findings Here we report an efficient and handy alternative for E. histolytica gene down-regulation mediated by bacterial double-stranded RNA (dsRNA) targeting parasite genes. The Escherichia coli strain HT115 which is unable to degrade dsRNA, was genetically engineered to produce high quantities of long dsRNA segments targeting the genes that encode E. histolytica β-tubulin and virulence factor KERP1. Trophozoites cultured in vitro were directly fed with dsRNA-expressing bacteria or soaked with purified dsRNA. Both dsRNA delivery methods resulted in significant reduction of protein expression. In vitro host cell-parasite assays showed that efficient downregulation of kerp1 gene expression mediated by bacterial dsRNA resulted in significant reduction of parasite adhesion and lytic capabilities, thus supporting a major role for KERP1 in the pathogenic process. Furthermore, treatment of trophozoites cultured in microtiter plates, with a repertoire of eighty-five distinct bacterial dsRNA segments targeting E. histolytica genes with unknown function, led to the identification of three genes potentially involved in the growth of the parasite. Conclusions Our results showed that the use of bacterial dsRNA is a powerful method for the study of gene function in E. histolytica. This dsRNA delivery method is also technically suitable for the study of a large number of genes, thus opening interesting perspectives for the identification of novel drug and vaccine targets.
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Affiliation(s)
- Carlos F. Solis
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Julien Santi-Rocca
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Doranda Perdomo
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Christian Weber
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Nancy Guillén
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
- * E-mail:
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22
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Crop improvement using small RNAs: applications and predictive ecological risk assessments. Trends Biotechnol 2009; 27:644-51. [DOI: 10.1016/j.tibtech.2009.08.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/31/2009] [Accepted: 08/17/2009] [Indexed: 01/31/2023]
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Xu X, Zhu D, Zhao Q, Ao G, Ma C, Yu J. RNA silencing mediated by direct repeats in maize: a potential tool for functional genomics. Mol Biotechnol 2008; 41:213-23. [PMID: 19031013 DOI: 10.1007/s12033-008-9124-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
It has been shown in tobacco and Arabidopsis that transgenes with multiple direct repeats induce RNA silencing at high frequency. In this study, we tried to establish a direct repeat-induced RNA silencing system in maize and evaluate whether it can be developed as a high throughput tool for functional genomics. Our results showed that the construct phC4, which carries four direct repeats of a chloramphenicol acetyl-transferase (CAT) gene, was able to induce silencing of itself with high efficiency in maize. Using a transient expression system, we further demonstrated that construct phC3G with a beta-glucuronidase (GUS) gene located downstream of three direct repeats of CAT gene silenced not only itself in maize calli but also an "endogenous" GUS gene, which was stably expressed in maize calli. Most importantly, when constructs with the maize iojap (ij) gene inserted in either sense or antisense orientation into the downstream of four direct repeats of CAT gene were transformed into maize plants, co-suppression of endogenous and transgenic ij genes was detected in majority of transgenic maize plants. Our co-suppression results suggest that with improvements, this new approach has the potential to become an efficient research tool for high throughput functional genomics.
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Affiliation(s)
- Xiuping Xu
- State Key Laboratory for Agro-biotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, People's Republic of China
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Silencing of six hydrophobins in Cladosporium fulvum: complexities of simultaneously targeting multiple genes. Appl Environ Microbiol 2008; 75:542-6. [PMID: 19011063 DOI: 10.1128/aem.01816-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we have constructed and expressed inverted repeat chimeras from the first exons of the six known hydrophobins of the fungus Cladosporium fulvum, the causal agent of tomato leaf mold. We used quantitative PCR to measure specifically the expression levels of the hydrophobins. The targeted genes are silenced to different degrees, but we also detected clear changes in the expression levels of nontargeted genes. This work highlights the difficulties that are likely to be encountered when attempting to silence more than one gene in a multigene family.
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