1
|
Ryu AJ, Jeong BR, Kang NK, Jeon S, Sohn MG, Yun HJ, Lim JM, Jeong SW, Park YI, Jeong WJ, Park S, Chang YK, Jeong KJ. Safe-Harboring based novel genetic toolkit for Nannochloropsis salina CCMP1776: Efficient overexpression of transgene via CRISPR/Cas9-Mediated Knock-in at the transcriptional hotspot. BIORESOURCE TECHNOLOGY 2021; 340:125676. [PMID: 34365302 DOI: 10.1016/j.biortech.2021.125676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Transgene expression in microalgae can be hampered by transgene silencing and unstable expression due to position effects. To overcome this, "safe harboring" transgene expression system was established for Nannochloropsis. Initially, transformants were obtained expressing a sfGFP reporter, followed by screening for high expression of sfGFP with fluorescence-activated cell sorter (FACS). 'T1' transcriptional hotspot was identified from a mutant showing best expression of sfGFP, but did not affect growth or lipid contents. By using a Cas9 editor strain, FAD12 gene, encoding Δ12-fatty acid desaturase (FAD12), was successfully knocked-in at the T1 locus, resulting in significantly higher expression of FAD12 than those of random integration. Importantly, the "safe harbored" FAD12 transformants showed four-fold higher production of linoleic acid (LA), the product of FAD12, leading to 1.5-fold increase in eicosapentaenoic acid (EPA). This safe harboring principle provide excellent proof of the concept for successful genetic/metabolic engineering of microalgae and other organisms.
Collapse
Affiliation(s)
- Ae Jin Ryu
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Byeong-Ryool Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Single-Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Qingdao, Shandong 266101, China
| | - Nam Kyu Kang
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Seungjib Jeon
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Min Gi Sohn
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyo Jin Yun
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jong Min Lim
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seok Won Jeong
- Department of Biological Sciences, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Won Joong Jeong
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| |
Collapse
|
2
|
Yuan L, Chen X, Chen H, Wu K, Huang S. Histone deacetylases HDA6 and HDA9 coordinately regulate valve cell elongation through affecting auxin signaling in Arabidopsis. Biochem Biophys Res Commun 2018; 508:695-700. [PMID: 30527808 DOI: 10.1016/j.bbrc.2018.11.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 10/27/2022]
Abstract
Both Histone Deacetylases HDA6 and HDA9 belong to class I subfamily of RPD3/HDA1 HDACs. Loss-of-function mutants of HDA9 form slightly blunt siliques. However, the involvement of HDA6 in regulating silique tip growth is unclear. In this study, we show that HDA6 acts redundantly with HDA9 in regulating the elongation of valve cells in the silique tip. Although the hda6 single mutant does not exhibit a detectable silique phenotype, the silique tip of hda6 hda9 double mutant displays a more severe bulge, a morphology we termed as "nock-shaped". The valve cells of the silique tip of hda9 are longer than wild-type, and loss of HDA6 in hda9 enhances the valve cell elongation phenotype. The transcript levels of auxin-signaling-related genes are mis-regulated in hda9 and hda6 hda9 siliques, and the GFP reporter driven by the auxin response promoter DR5 is weaker in hda9 or hda6 hda9 than wild-type or hda6. Thus, our findings reveal that HDA6 and HDA9 coordinately control the elongation of silique valve cells through regulating the expression of auxin-related genes in silique tips.
Collapse
Affiliation(s)
- Liangbing Yuan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xue Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Huhui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
| |
Collapse
|
3
|
Abstract
Assessing molecular changes that occur through altering a gene's activity is often hampered by difficulties that arise due to the typically static nature of the introduced perturbation. This is especially problematic when investigating molecular events at specific stages and/or in certain tissues or organs during Arabidopsis development. To circumvent these issues, we have employed chemically inducible artificial microRNAs (amiRNAs) for the specific knockdown of developmental regulators. For our own research, we have combined this gene perturbation approach with a floral induction system, which allows the simultaneous induction of a large number of flowers on the inflorescence of a single plant, and the ability to knock down a gene's activity at any given stage of development. To enable the plant community to avail of the full benefits of these systems, we describe, in this chapter, strategies for amiRNA-mediated gene perturbations and address some common problems that can be encountered when generating inducible amiRNA constructs, growing these plants, and collecting floral buds for analysis.
Collapse
|
4
|
Yang X, Niu L, Zhang W, Yang J, Xing G, He H, Guo D, Du Q, Qian X, Yao Y, Li Q, Dong Y. RNAi-mediated SMV P3 cistron silencing confers significantly enhanced resistance to multiple Potyvirus strains and isolates in transgenic soybean. PLANT CELL REPORTS 2018; 37:103-114. [PMID: 28756582 DOI: 10.1007/s00299-017-2186-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/18/2017] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE Robust RNAi-mediated resistance to multiple Potyvirus strains and isolates, but not to Secovirus BPMV, was conferred by expressing a short SMV P3 hairpin in soybean plants. Engineering resistance to multiple Potyvirus strains is of great interest because of a wide variability of the virus strains, and mixed infections of multiple viruses or strains commonly associated with field grown soybean. In this study, RNAi-mediated silencing of the soybean mosaic virus (SMV) P3 cistron, which is reported to participate in virus movements and pathogenesis and to be the putative determinant of SMV virulence, was used to induce resistance to multiple Potyvirus strains and isolates in soybean. A 302 bp inverted repeat (IR) of the P3 cistron, isolated from the SMV strain SC3, was introduced into soybean. The transgenic lines exhibited stable and enhanced resistance to SMV SC3 under field conditions over 3 consecutive years. The transgenic lines also showed significantly enhanced resistance to four other SMV strains (SC7, SC15, SC18, and SMV-R, a novel recombinant found in China), the soybean-infecting bean common mosaic virus (BCMV) and watermelon mosaic virus (WMV). Nevertheless, no significant differences were found between transgenic plants and their non-transformed (NT) counterparts in terms of resistance to bean pod mottle virus (BPMV, Secoviridae). Consistent with the results of resistance evaluations, the expression of the respective viral CP cistrons and virus accumulation were significantly lower in seven Potyvirus strains and isolates than in the NT plants, but not in BCMV-inoculated transgenic lines. The results demonstrate the effectiveness of engineering resistance to multiple Potyvirus strains and isolates via RNAi-mediated SMV P3 cistron silencing, and thus provide an effective control strategy against Potyvirus infections in soybean and other crops.
Collapse
Affiliation(s)
- Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lu Niu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Wei Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jing Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Guojie Xing
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Hongli He
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Dongquan Guo
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qian Du
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xueyan Qian
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yao Yao
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qiyun Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| |
Collapse
|
5
|
Yang X, Niu L, Zhang W, He H, Yang J, Xing G, Guo D, Du Q, Qian X, Yao Y, Li Q, Dong Y. Robust RNAi-mediated resistance to infection of seven potyvirids in soybean expressing an intron hairpin NIb RNA. Transgenic Res 2017; 26:665-676. [PMID: 28840434 DOI: 10.1007/s11248-017-0041-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/21/2017] [Indexed: 12/31/2022]
Abstract
Viral pathogens, such as soybean mosaic virus (SMV), are a major constraint in soybean production and often cause significant yield loss and quality deterioration. Engineering resistance by RNAi-mediated gene silencing is a powerful strategy for controlling viral diseases. In this study, a 248-bp inverted repeat of the replicase (nuclear inclusion b, NIb) gene was isolated from the SMV SC3 strain, driven by the leaf-specific rbcS2 promoter from Phaseolus vulgaris, and introduced into soybean. The transgenic lines had significantly lower average disease indices (ranging from 2.14 to 12.35) than did the non-transformed (NT) control plants in three consecutive generations, exhibiting a stable and significantly enhanced resistance to the SMV SC3 strain under field conditions. Furthermore, seed mottling did not occur in transgenic seeds, whereas the NT plants produced ~90% mottled seeds. Virus resistance spectrum screening showed that the greenhouse-grown transgenic lines exhibited robust resistance to five SMV strains (SC3, SC7, SC15, SC18, and a recombinant SMV), bean common mosaic virus, and watermelon mosaic virus. Nevertheless, no significantly enhanced resistance to bean pod mottle virus (BPMV, Comovirus) was observed in the transgenic lines relative to their NT counterparts. Consistent with the results of resistance evaluation, the accumulation of each potyvirid (but not of BPMV) was significantly inhibited in the transgenic plants relative to the NT controls as confirmed by quantitative real-time (qRT-PCR) and double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). These results demonstrate that robust RNAi-mediated resistance to multiple potyvirids in soybean was conferred by expressing an intron hairpin SMV NIb RNA.
Collapse
Affiliation(s)
- Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lu Niu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Wei Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Hongli He
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jing Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Guojie Xing
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Dongquan Guo
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qian Du
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xueyan Qian
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yao Yao
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qiyun Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| |
Collapse
|
6
|
Streubel J, Baum H, Grau J, Stuttman J, Boch J. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017; 12:e0173580. [PMID: 28301511 PMCID: PMC5354296 DOI: 10.1371/journal.pone.0173580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.
Collapse
Affiliation(s)
- Jana Streubel
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Heidi Baum
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute of Computer Science, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Johannes Stuttman
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| |
Collapse
|
7
|
Beacham TA, Ali ST. Growth dependent silencing and resetting of DGA1 transgene in Nannochloropsis salina. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
8
|
Sekan AS, Isayenkov SV, Blume YB. Development of marker-free transformants by site-specific recombinases. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715060080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Rajeevkumar S, Anunanthini P, Sathishkumar R. Epigenetic silencing in transgenic plants. FRONTIERS IN PLANT SCIENCE 2015; 6:693. [PMID: 26442010 PMCID: PMC4564723 DOI: 10.3389/fpls.2015.00693] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/21/2015] [Indexed: 05/18/2023]
Abstract
Epigenetic silencing is a natural phenomenon in which the expression of genes is regulated through modifications of DNA, RNA, or histone proteins. It is a mechanism for defending host genomes against the effects of transposable elements and viral infection, and acts as a modulator of expression of duplicated gene family members and as a silencer of transgenes. A major breakthrough in understanding the mechanism of epigenetic silencing was the discovery of silencing in transgenic tobacco plants due to the interaction between two homologous promoters. The molecular mechanism of epigenetic mechanism is highly complicated and it is not completely understood yet. Two different molecular routes have been proposed for this, that is, transcriptional gene silencing, which is associated with heavy methylation of promoter regions and blocks the transcription of transgenes, and post-transcriptional gene silencing (PTGS), the basic mechanism is degradation of the cytosolic mRNA of transgenes or endogenous genes. Undesired transgene silencing is of major concern in the transgenic technologies used in crop improvement. A complete understanding of this phenomenon will be very useful for transgenic applications, where silencing of specific genes is required. The current status of epigenetic silencing in transgenic technology is discussed and summarized in this mini-review.
Collapse
Affiliation(s)
- Sarma Rajeevkumar
- Molecular Plant Biology and Biotechnology Division, Central Institute of Medicinal and Aromatic Plants Research Centre, BangaloreIndia
| | - Pushpanathan Anunanthini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, CoimbatoreIndia
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, CoimbatoreIndia
| |
Collapse
|
10
|
Lee HG, Lee K, Jang K, Seo PJ. Circadian expression profiles of chromatin remodeling factor genes in Arabidopsis. JOURNAL OF PLANT RESEARCH 2015; 128:187-99. [PMID: 25315904 DOI: 10.1007/s10265-014-0665-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/25/2014] [Indexed: 05/13/2023]
Abstract
The circadian clock is a biological time keeper mechanism that regulates biological rhythms to a period of approximately 24 h. The circadian clock enables organisms to anticipate environmental cycles and coordinates internal cellular physiology with external environmental cues. In plants, correct matching of the clock with the environment confers fitness advantages to plant survival and reproduction. Therefore, circadian clock components are regulated at multiple layers to fine-tune the circadian oscillation. Epigenetic regulation provides an additional layer of circadian control. However, little is known about which chromatin remodeling factors are responsible for circadian control. In this work, we analyzed circadian expression of 109 chromatin remodeling factor genes and identified 17 genes that display circadian oscillation. In addition, we also found that a candidate interacts with a core clock component, supporting that clock activity is regulated in part by chromatin modification. As an initial attempt to elucidate the relationship between chromatin modification and circadian oscillation, we identified novel regulatory candidates that provide a platform for future investigations of chromatin regulation of the circadian clock.
Collapse
Affiliation(s)
- Hong Gil Lee
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju, 561-756, Korea
| | | | | | | |
Collapse
|
11
|
Abstract
Cre/LoxP has broad utility for studying the function, development, and oncogenic transformation of pancreatic cells in mice. Here we provide an overview of the Cre driver lines that are available for such studies. We discuss how variegated expression, transgene silencing, and recombination in undesired cell types have conspired to limit the performance of these lines, sometimes leading to serious experimental concerns. We also discuss preferred strategies for achieving high-fidelity driver lines and remind investigators of the continuing need for caution when interpreting results obtained from any Cre/LoxP-based experiment performed in mice.
Collapse
Affiliation(s)
- Mark A Magnuson
- Center for Stem Cell Biology and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | | |
Collapse
|
12
|
Singhabahu S, George J, Bringloe D. Expression of a functional human adenosine deaminase in transgenic tobacco plants. Transgenic Res 2013; 22:643-9. [PMID: 23264022 DOI: 10.1007/s11248-012-9676-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 12/06/2012] [Indexed: 11/28/2022]
Abstract
An inherited disorder, adenosine deaminase deficiency is a form of severe combined immunodeficiency, which is ultimately caused by an absence of adenosine deaminase (ADA), a key enzyme of the purine salvage pathway. The absence of ADA-activity in sufferers eventually results in a dysfunctional immune system due to the build-up of toxic metabolites. To date, this has been treated with mixed success, using PEG-ADA, made from purified bovine ADA coupled to polyethylene glycol. It is likely, however, that an enzyme replacement therapy protocol based on recombinant human ADA would be a more effective treatment for this disease. Therefore, as a preliminary step to produce biologically active human ADA in transgenic tobacco plants a human ADA cDNA has been inserted into a plant expression vector under the control of the CaMV 35S promoter and both human and TMV 5' UTR control regions. Plant vector expression constructs have been used to transform tobacco plants via Agrobacterium-mediated transformation. Genomic DNA, RNA and protein blot analyses have demonstrated the integration of the cDNA construct into the plant nuclear genome and the expression of recombinant ADA mRNA and protein in transgenic tobacco leaves. Western blot analysis has also revealed that human and recombinant ADA have a similar size of approximately 41 kDa. ADA-specific activities of between 0.001 and 0.003 units per mg total soluble protein were measured in crude extracts isolated from transformed tobacco plant leaves.
Collapse
Affiliation(s)
- Sanjeewa Singhabahu
- School of Health, Sport and Bioscience, University of East London, Water Lane, London E15 4LZ, UK
| | | | | |
Collapse
|
13
|
Schornack S, Moscou MJ, Ward ER, Horvath DM. Engineering plant disease resistance based on TAL effectors. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:383-406. [PMID: 23725472 DOI: 10.1146/annurev-phyto-082712-102255] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transcription activator-like (TAL) effectors are encoded by plant-pathogenic bacteria and induce expression of plant host genes. TAL effectors bind DNA on the basis of a unique code that specifies binding of amino acid residues in repeat units to particular DNA bases in a one-to-one correspondence. This code can be used to predict binding sites of natural TAL effectors and to design novel synthetic DNA-binding domains for targeted genome manipulation. Natural mechanisms of resistance in plants against TAL effector-containing pathogens have given insights into new strategies for disease control.
Collapse
Affiliation(s)
- Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, United Kingdom
| | | | | | | |
Collapse
|
14
|
Scientific opinion addressing the safety assessment of plants developed through cisgenesis and intragenesis. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2561] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
15
|
Wang Y, Yau YY, Perkins-Balding D, Thomson JG. Recombinase technology: applications and possibilities. PLANT CELL REPORTS 2011; 30:267-85. [PMID: 20972794 PMCID: PMC3036822 DOI: 10.1007/s00299-010-0938-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/08/2010] [Indexed: 05/02/2023]
Abstract
The use of recombinases for genomic engineering is no longer a new technology. In fact, this technology has entered its third decade since the initial discovery that recombinases function in heterologous systems (Sauer in Mol Cell Biol 7(6):2087-2096, 1987). The random insertion of a transgene into a plant genome by traditional methods generates unpredictable expression patterns. This feature of transgenesis makes screening for functional lines with predictable expression labor intensive and time consuming. Furthermore, an antibiotic resistance gene is often left in the final product and the potential escape of such resistance markers into the environment and their potential consumption raises consumer concern. The use of site-specific recombination technology in plant genome manipulation has been demonstrated to effectively resolve complex transgene insertions to single copy, remove unwanted DNA, and precisely insert DNA into known genomic target sites. Recombinases have also been demonstrated capable of site-specific recombination within non-nuclear targets, such as the plastid genome of tobacco. Here, we review multiple uses of site-specific recombination and their application toward plant genomic engineering. We also provide alternative strategies for the combined use of multiple site-specific recombinase systems for genome engineering to precisely insert transgenes into a pre-determined locus, and removal of unwanted selectable marker genes.
Collapse
Affiliation(s)
- Yueju Wang
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
| | - Yuan-Yeu Yau
- Department of Plant and Microbial Biology, Plant Gene Expression Center, USDA-ARS, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710 USA
| | | | - James G. Thomson
- Crop Improvement and Utilization Unit, USDA-ARS WRRC, 800 Buchanan St., Albany, CA 94710 USA
| |
Collapse
|
16
|
Filipenko EA, Deineko EV, Shumnyi VK. Specific features of T-DNA insertion regions in transgenic plants. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Rawat P, Kumar S, Pental D, Burma PK. Inactivation of a transgene due to transposition of insertion sequence (IS136) of Agrobacterium tumefaciens. J Biosci 2009; 34:199-202. [PMID: 19550035 DOI: 10.1007/s12038-009-0023-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Agrobacterium strains harbour insertion sequences, which are known to transpose into genomes as well as into Ti plasmids. In this study we report the inactivation of a transgene due to transposition of the A. tumefaciens insertion sequence IS136. The transposition was discovered following transformation of plant tissues, although the fidelity of the binary vector was confirmed following transformation into Agrobacterium. Such transpositions are rare but can occur and it is thus important to check the fidelity of the binary vector at different times of Agrobacterium growth in order to avoid failure in achieving transgene expression.
Collapse
Affiliation(s)
- Preeti Rawat
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | | | | | | |
Collapse
|
18
|
Niu C, Akasaka-Kennedy Y, Faustinelli P, Joshi M, Rajasekaran K, Yang H, Chu Y, Cary J, Ozias-Akins P. Antifungal Activity in Transgenic Peanut (Arachis hypogaea L.) Conferred by a Nonheme Chloroperoxidase Gene. ACTA ACUST UNITED AC 2009. [DOI: 10.3146/ps08-020.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract
A nonheme chloroperoxidase gene (cpo-p) from Pseudomonas pyrrocinia, a growth inhibitor of mycotoxin-producing fungi, was introduced into peanut via particle bombardment. The expression of the cpo-p gene is predicted to increase pathogen defense in peanut. Embryogenic peanut tissues were bombarded with gold particles coated with plasmid pRT66 carrying the cpo-p and hygromycin phosphotransferase (hph) genes, under the control of a double CaMV 35S and a single CaMV 35S promoter, respectively. Selection for hygromycin-resistant somatic embryos was performed on a liquid medium containing 10–20 mg/L hygromycin 3–4 days after bombardment. The integration and expression of the cpo-p gene was confirmed by Southern, Northern and Western blot analyses. In vitro bioassay using crude protein extracts from transgenic T0, T1, and T4 plants showed inhibition of Aspergillus flavus hyphal growth, which could translate to a reduction in aflatoxin contamination of peanut seed.
Collapse
|
19
|
Nanto K, Sato K, Katayama Y, Ebinuma H. Expression of a transgene exchanged by the recombinase-mediated cassette exchange (RMCE) method in plants. PLANT CELL REPORTS 2009; 28:777-85. [PMID: 19241079 DOI: 10.1007/s00299-009-0683-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Revised: 01/31/2009] [Accepted: 02/04/2009] [Indexed: 05/09/2023]
Abstract
We developed a site-directed integration (SDI) system for Agrobacterium-mediated transformation to precisely integrate a single copy of a desired gene into a predefined target locus by recombinase-mediated cassette exchange (RMCE). We produced site-specific transgenic tobacco plants from four target lines and examined expression of the transgene in T1 site-specific transgenic tobacco plants, which were obtained by backcrossing. We found that site-specific transgenic plants from the same target lines showed approximately the same level of expression of the transgene. Moreover, we demonstrated that site-specific transgenic plants showed much less variability of transgene expression than random-integration transgenic plants. Interestingly, transgenes in the same direction at the same target locus showed the same level of activity, but transgenes in different directions showed different levels of activity. The expression levels of transgene did not correlate with those of the target gene. Our results showed that the SDI system could benefit the precise comparisons between different gene constructs, the characterization of different chromosomal regions and the cost-effective screening of reliable transgenic plants.
Collapse
Affiliation(s)
- Kazuya Nanto
- Forestly Science Laboratory, Nippon Paper Industries Co., Ltd, Kita-ku, Tokyo, Japan
| | | | | | | |
Collapse
|
20
|
Xiao BZ, Chen X, Xiang CB, Tang N, Zhang QF, Xiong LZ. Evaluation of seven function-known candidate genes for their effects on improving drought resistance of transgenic rice under field conditions. MOLECULAR PLANT 2009; 2:73-83. [PMID: 19529831 PMCID: PMC2639742 DOI: 10.1093/mp/ssn068] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 09/19/2008] [Indexed: 05/18/2023]
Abstract
Many stress responsive genes have been reported with an effect on improving stress resistance in model plants under greenhouse conditions. Towards identification of genes for drought resistance breeding, seven well documented genes (CBF3, SOS2, NCED2, NPK1, LOS5, ZAT10, and NHX1) in stress resistance were selected in this study and transformed into rice cultivar Zhonghua 11 under the control of constitutive promoter Actin1 and stress-inducible promoter of a rice HVA22 homolog, and transgenic rice were tested for drought resistance under field conditions. A total of 1598 independent transgenic T0 plants were generated. The percentages of single copy and expression of the transgenes were 36.7% and 57.6%, respectively. For each gene construct, 30 T1 families with expression of transgene were selected for drought resistance testing at the reproductive stage in field, and 10 of them were tested in PVC pipes with a defined stress protocol at the same stage. Relative yield and relative spikelet fertility were used as two major criteria to evaluate drought resistance performance because significantly decreased yield was observed in the T1 generation. Transgenic families of eight constructs (HVA22P:CBF3, HVA22P:NPK1, Actin1:LOS5, HVA22P:LOS5, Actin1:ZAT10, HVA22P:ZAT10, Actin1:NHX1, and HVA22P:NHX1) showed significantly higher RY than wild-type (WT) under both drought stress field and PVC tube conditions. Transgenic families of 9 constructs (HVA22P:SOS2 and CBF3, LOS5, ZAT10, and NHX1 by both promoters) showed significantly higher relative spikelet fertility than WT in the field or PVC pipes. In the field drought resistance testing of T2 families derived from the T1 families with relatively lower yield decrease, transgenic families of seven constructs (HVA22P:CBF3, Actin1:NPK1, HVA22P:NPK1, Actin1:LOS5, HVA22P:LOS5, Actin1:ZAT10, and HVA22P:ZAT10) showed significantly higher yield per plant than WT, and families of nine constructs (Actin1:CBF3, HVA22P:CBF3, HVA22P:SOS2, HVA22P:NPK1, Actin1:LOS5, HVA22P:LOS5, Actin1:ZAT10, HVA22P:ZAT10, and Actin1:NHX1) had higher spikelet fertility than WT. In general, LOS5 and ZAT10 showed relatively better effect than the other five genes in improving drought resistance of transgenic rice under field conditions. The results and experience obtained from this study could be a useful reference for drought resistance engineering in rice.
Collapse
Affiliation(s)
- Ben-Ze Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Cheng-Bin Xiang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Ning Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi-Fa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Li-Zhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- To whom correspondence should be addressed. E-mail , fax 86-27-87287092, tel. 86-27-87281536
| |
Collapse
|
21
|
Nanto K, Ebinuma H. Marker-free site-specific integration plants. Transgenic Res 2007; 17:337-44. [PMID: 17588210 DOI: 10.1007/s11248-007-9106-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Recently, site-specific recombination methods in plants have been developed to delete selection markers to produce marker-free transgenic plants or to integrate the transgene into a pre-determined genomic location to produce site-specific transgenic plants. However, these methods have been developed independently, and although the strategies of producing marker-free site-specific integration plants have been discussed, the concept has not been demonstrated. In the present study, we combined two approaches to site-specific recombination and demonstrated the concepts for removing the marker after site-specific integration for producing marker-free site-specific transgenic plants.
Collapse
Affiliation(s)
- Kazuya Nanto
- Forestry Science Research Laboratory, Nippon Paper Industries Co., Ltd., 5-21-1, Oji, Kita-ku, Tokyo 114-0002, Japan
| | | |
Collapse
|
22
|
Xiao B, Huang Y, Tang N, Xiong L. Over-expression of a LEA gene in rice improves drought resistance under the field conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:35-46. [PMID: 17426956 DOI: 10.1007/s00122-007-0538-9] [Citation(s) in RCA: 260] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 03/17/2007] [Indexed: 05/14/2023]
Abstract
Late embryogenesis abundant (LEA) proteins have been implicated in many stress responses of plants. In this report, a LEA protein gene OsLEA3-1 was identified and over-expressed in rice to test the drought resistance of transgenic lines under the field conditions. OsLEA3-1 is induced by drought, salt and abscisic acid (ABA), but not by cold stress. The promoter of OsLEA3-1 isolated from the upland rice IRAT109 exhibits strong activity under drought- and salt-stress conditions. Three expression constructs consisting of the full-length cDNA driven by the drought-inducible promoter of OsLEA3-1 (OsLEA3-H), the CaMV 35S promoter (OsLEA3-S), and the rice Actin1 promoter (OsLEA3-A) were transformed into the drought-sensitive japonica rice Zhonghua 11. Drought resistance pre-screening of T(1) families at anthesis stage revealed that the over-expressing families with OsLEA3-S and OsLEA3-H constructs had significantly higher relative yield (yield under drought stress treatment/yield under normal growth conditions) than the wild type under drought stress conditions, although a yield penalty existed in T(1) families under normal growth conditions. Nine homozygous families, exhibiting over-expression of a single-copy of the transgene and relatively low yield penalty in the T(1) generation, were tested in the field for drought resistance in the T(2) and T(3) generations and in the PVC pipes for drought tolerance in the T(2) generation. Except for two families (transformed with OsLEA3-A), all the other families (transformed with OsLEA3-S and OsLEA3-H constructs) had higher grain yield than the wild type under drought stress in both the field and the PVC pipes conditions. No significant yield penalty was detected for these T(2 )and T(3) families. These results indicate that transgenic rice with significantly enhanced drought resistance and without yield penalty can be generated by over-expressing OsLEA3-1 gene with appropriate promoters and following a bipartite (stress and non-stress) in-field screening protocol.
Collapse
Affiliation(s)
- Benze Xiao
- National Center of Plant Gene Research (Wuhan), National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | |
Collapse
|
23
|
Over-expression of a LEA gene in rice improves drought resistance under the field conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007. [PMID: 17426956 DOI: 10.1007/s00122‐007‐0538‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Late embryogenesis abundant (LEA) proteins have been implicated in many stress responses of plants. In this report, a LEA protein gene OsLEA3-1 was identified and over-expressed in rice to test the drought resistance of transgenic lines under the field conditions. OsLEA3-1 is induced by drought, salt and abscisic acid (ABA), but not by cold stress. The promoter of OsLEA3-1 isolated from the upland rice IRAT109 exhibits strong activity under drought- and salt-stress conditions. Three expression constructs consisting of the full-length cDNA driven by the drought-inducible promoter of OsLEA3-1 (OsLEA3-H), the CaMV 35S promoter (OsLEA3-S), and the rice Actin1 promoter (OsLEA3-A) were transformed into the drought-sensitive japonica rice Zhonghua 11. Drought resistance pre-screening of T(1) families at anthesis stage revealed that the over-expressing families with OsLEA3-S and OsLEA3-H constructs had significantly higher relative yield (yield under drought stress treatment/yield under normal growth conditions) than the wild type under drought stress conditions, although a yield penalty existed in T(1) families under normal growth conditions. Nine homozygous families, exhibiting over-expression of a single-copy of the transgene and relatively low yield penalty in the T(1) generation, were tested in the field for drought resistance in the T(2) and T(3) generations and in the PVC pipes for drought tolerance in the T(2) generation. Except for two families (transformed with OsLEA3-A), all the other families (transformed with OsLEA3-S and OsLEA3-H constructs) had higher grain yield than the wild type under drought stress in both the field and the PVC pipes conditions. No significant yield penalty was detected for these T(2 )and T(3) families. These results indicate that transgenic rice with significantly enhanced drought resistance and without yield penalty can be generated by over-expressing OsLEA3-1 gene with appropriate promoters and following a bipartite (stress and non-stress) in-field screening protocol.
Collapse
|
24
|
Chen HJ, Wang SJ, Chen CC, Yeh KW. New gene construction strategy in T-DNA vector to enhance expression level of sweet potato sporamin and insect resistance in transgenic Brassica oleracea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2006; 171:367-374. [PMID: 22980206 DOI: 10.1016/j.plantsci.2006.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 04/01/2006] [Accepted: 04/16/2006] [Indexed: 06/01/2023]
Abstract
Sporamin, an abundant storage protein in tuberous roots of sweet potato, possesses strong inhibitory activity against trypsin and pest-resistance. To promote consistent high-level expression of sporamin and insect resistance in transgenic Brassica plants, a wound-responsive sporamin promoter (Pspoa) alone or combined with matrix-attached-region-like DNA segment (spoMAR) were constructed for driving sporamin cDNA. The results showed the transgenic plants containing Pspoa-drived sporamin and spoMAR displayed the highest level and low inter-transformant variability of sporamin expression, and the ability of insect resistance of transformants positively correlated with sporamin activity. Furthermore, expressions of Pspoa-drived sporamin especially combined with the spoaMAR retains high and steady levels in the T(1) and T(2) generations, in marked contrast to the variable expression patterns observed in CaMV35S promoter-driven transformants. This study evidently indicates that the Pspoa and spoaMAR would be very efficient for high transgene expression in plants and obtaining inherently stable transformants in consecutive progenies.
Collapse
Affiliation(s)
- Huai-Ju Chen
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | | | | | | |
Collapse
|
25
|
McGinnis KM, Springer C, Lin Y, Carey CC, Chandler V. Transcriptionally silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics 2006; 173:1637-47. [PMID: 16702420 PMCID: PMC1526669 DOI: 10.1534/genetics.106.058669] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 05/09/2006] [Indexed: 11/18/2022] Open
Abstract
Plants with mutations in one of three maize genes, mop1, rmr1, and rmr2, are defective in paramutation, an allele-specific interaction that leads to meiotically heritable chromatin changes. Experiments reported here demonstrate that these genes are required to maintain the transcriptional silencing of two different transgenes, suggesting that paramutation and transcriptional silencing of transgenes share mechanisms. We hypothesize that the transgenes are silenced through an RNA-directed chromatin mechanism, because mop1 encodes an RNA-dependent RNA polymerase. In all the mutants, DNA methylation was reduced in the active transgenes relative to the silent transgenes at all of the CNG sites monitored within the transgene promoter. However, asymmetrical methylation persisted at one site within the reactivated transgene in the rmr1-1 mutant. With that one mutant, rmr1-1, the transgene was efficiently resilenced upon outcrossing to reintroduce the wild-type protein. In contrast, with the mop1-1 and rmr2-1 mutants, the transgene remained active in a subset of progeny even after the wild-type proteins were reintroduced by outcrossing. Interestingly, this immunity to silencing increased as the generations progressed, consistent with a heritable chromatin state being formed at the transgene in plants carrying the mop1-1 and rmr2-1 mutations that becomes more resistant to silencing in subsequent generations.
Collapse
Affiliation(s)
- Karen M McGinnis
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | | | |
Collapse
|
26
|
Oard SV, Enright FM. Expression of the antimicrobial peptides in plants to control phytopathogenic bacteria and fungi. PLANT CELL REPORTS 2006; 25:561-72. [PMID: 16456649 DOI: 10.1007/s00299-005-0102-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Revised: 11/01/2005] [Accepted: 11/20/2005] [Indexed: 05/06/2023]
Abstract
Three antimicrobial peptides exhibiting in vitro antifungal activity were expressed in Arabidopsis to compare their in planta activity. Beta-Purothionin, cecropin B, and phor21 were expressed under an endogenous promoter with moderate-level activity and excreted extracellularly. Expression of beta-purothionin rendered the greatest antibacterial and antifungal resistance while cecropin B enhanced only antibacterial activity and phor21 did not improve antimicrobial resistance. The transgenic beta-purothionin arrested fungal growth on leaf surfaces and infection of stomata. Leaf extracts from plants producing beta-purothionin and cecropin B displayed membrane permeabilizing activity. The in planta antimicrobial activity of the tested peptides was consistent with previously reported in vitro experiments. The expression strategy allowed enhanced antifungal resistance without high-level transgene expression.
Collapse
Affiliation(s)
- S V Oard
- LSU AgCenter Biotechnology Laboratory, Louisiana State University, 115 Wilson Bldg., Baton Rouge, LA 70803, USA.
| | | |
Collapse
|
27
|
El-Shemy HA, Khalafalla MM, Fujita K, Ishimoto M. Molecular control of gene co-suppression in transgenic soybean via particle bombardment. JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2006; 39:61-7. [PMID: 16466639 DOI: 10.5483/bmbrep.2006.39.1.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Molecular co-suppression phenomena are important to consider in transgene experiments. Embryogenic cells were obtained from immature cotyledons and engineered with two different gene constructs (pHV and pHVS) through particle bombardment. Both constructs contain a gene conferring resistance to hygromycin (hpt) as a selective marker and a modified glycinin (11S globulin) gene (V3-1) as a target. sGFP(S65T) as a reporter gene was, however, inserted into the flanking region of the V3-1 gene (pHVS). Fluorescence microscopic screening after the selection of hygromycin, identified clearly the expression of sGFP(S65T) in the transformed soybean embryos bombarded with the pHVS construct. Stable integration of the transgenes was confirmed by polymerase chain reaction (PCR) and Southern blot analysis. Seeds of transgenic plants obtained from the pHV construct frequently lacked an accumulation of endogenous glycinin, which is encoded by homologous genes to the target gene V3-1. Most of the transgenic plants expressing sGFP(S65T) showed highly accumulation of glycinin. The expression of sGFP(S65T) and V3-1 inherits into the next generations. sGFP(S65T) as a reporter gene may be useful to increase the transformation efficiency of transgenic soybean with avoiding gene co-suppression.
Collapse
Affiliation(s)
- Hany A El-Shemy
- National Agricultural Research Center for Western Region, 6-12-1 Nishifukatsu, Fukuyama, Hiroshima, 721-8514, Japan.
| | | | | | | |
Collapse
|
28
|
Kerbach S, Lörz H, Becker D. Site-specific recombination in Zea mays. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1608-16. [PMID: 16200415 DOI: 10.1007/s00122-005-0092-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 08/22/2005] [Indexed: 05/04/2023]
Abstract
The elimination of marker genes after selection is recommended for the commercial use of genetically modified plants. We compared the applicability of the two site-specific recombination systems Cre/lox and Flp/FRT for marker gene elimination in maize plants. The selection marker gene pat surrounded by two identically directed lox or FRT sites was introduced into maize. Sexual crossing with plants harboring the corresponding constitutively expressed recombinase led to the precise and complete excision of the lox-flanked marker gene in the F1 progeny, whereas Flp-mediated recombination of FRT sequences occurred rarely. Further examination of site-specific integration was done by biolistic bombardment of immature embryos harboring only one lox site with a lox.uidA sequence with results indicating directed integration.
Collapse
Affiliation(s)
- S Kerbach
- Biocenter Klein Flottbek, Section Developmental Biology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | | | | |
Collapse
|
29
|
Masclaux FG, Pont-Lezica R, Galaud JP. Relationship between allelic state of T-DNA and DNA methylation of chromosomal integration region in transformed Arabidopsis thaliana plants. PLANT MOLECULAR BIOLOGY 2005; 58:295-303. [PMID: 16021396 DOI: 10.1007/s11103-005-4808-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 03/31/2005] [Indexed: 05/03/2023]
Abstract
T-DNA insertions are currently used as a tool to introduce, or knock out, specific genes. The expression of the inserted gene is frequently haphazard and up to now, it was proposed that transgene expression depends on the site of insertion within the genome, as well as the number of copies of the transgene. In this paper, we show that the allelic state of a T-DNA insertion can be at the origin of epigenetic silencing. A T-DNA insertional mutant was characterized to explore the function of AtBP80a', a vacuolar sorting receptor previously associated with germination. Seeds homozygous for the T-DNA do not germinate, but this can be overcome by a cold treatment and maintained by the following generations. The non-germinating phenotype is only observed in homozygous seed produced by heterozygous plants indicating that it is correlated with the allelic state of the T-DNA in parental lines. Analysis of the region between the T-DNA insertion and the ATG codon of atbp80a' showed that cytosine methylation is highly enhanced in chromatin containing the T-DNA. Data presented here show that an unpaired DNA region during meiosis could be at the origin of a de novo cytosine methylation mechanism.
Collapse
Affiliation(s)
- Frédéric G Masclaux
- UMR 5546 CNRS-Université Paul Sabatier, Pôle de Biotechnologie végétale, 24 chemin de Borde-Rouge, BP42617, 31326 Castanet-Tolosan, France
| | | | | |
Collapse
|
30
|
Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW. Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 2005; 6:R52. [PMID: 15960804 PMCID: PMC1175972 DOI: 10.1186/gb-2005-6-6-r52] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 04/01/2005] [Accepted: 04/25/2005] [Indexed: 11/17/2022] Open
Abstract
A transcriptome analysis of chromosome 10 of 2 rice subspecies identifies 549 new gene models and gives experimental evidence for around 75% of the previously unsupported predicted genes.
Background Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. Results We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. Conclusion These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice.
Collapse
MESH Headings
- Chromosomes, Plant/chemistry
- Chromosomes, Plant/genetics
- Cloning, Molecular
- Gene Expression Profiling
- Gene Expression Regulation, Plant/genetics
- Genes, Plant/genetics
- Models, Genetic
- Oligonucleotide Array Sequence Analysis
- Oryza/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Transcription, Genetic/genetics
Collapse
Affiliation(s)
- Lei Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Xiangfeng Wang
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
- Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Mian Xia
- National Center of Crop Design, China Bioway Biotech Group Co., LTD, Beijing 100085, China
| | - Viktor Stolc
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Genome Research Facility, NASA Ames Research Center, MS 239-11, Moffett Field, CA 94035, USA
| | - Ning Su
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Zhiyu Peng
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
| | - Songgang Li
- Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiping Wang
- National Center of Crop Design, China Bioway Biotech Group Co., LTD, Beijing 100085, China
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
31
|
Gerats T, Vandenbussche M. A model system for comparative research: Petunia. TRENDS IN PLANT SCIENCE 2005; 10:251-6. [PMID: 15882658 DOI: 10.1016/j.tplants.2005.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Research today aims to analyse the development of plant processes over evolutionary time. To obtain a representative view, a range of plant species covering at least the crucial nodes in phylogeny must be selected for an in depth analysis. Here we present Petunia as one of the available systems: as a representative of the Solanaceae it has the advantages of good culture conditions and the availability of a range of materials, techniques and strategies that can be used to research an interesting and diverse set of questions.
Collapse
Affiliation(s)
- Tom Gerats
- IWWR, Plant Genetics, Radboud University, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
| | | |
Collapse
|
32
|
Albertin W, Brabant P, Catrice O, Eber F, Jenczewski E, Chèvre AM, Thiellement H. Autopolyploidy in cabbage (Brassica oleracea L.) does not alter significantly the proteomes of green tissues. Proteomics 2005; 5:2131-9. [PMID: 15852348 DOI: 10.1002/pmic.200401092] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyploidization is a major evolutionary process in eukaryotes. In plants, genetic and epigenetic changes occur rapidly after formation of allopolyploids. Hybridization, rather than genome doubling itself, is considered as the main cause for the resulting differential gene expression. We studied the consequences of genome doubling alone in an autopolyploid model, by comparing two-dimensional gel electrophoresis (2-DE) gels of haploid, diploid, and tetraploid Brassica oleracea cabbages. Two fully homozygous lines, HDEM and RC, as well as two organs, leaf and stem, were studied. For the 558 common spots found present in all the 29 2-DE gels of the experiment, inter-organ and -genotype differences were the major sources of the variation in protein amounts: 41 and 10-13%, respectively. HDEM leaf and stem proteomes were not significantly affected by the ploidy level, since no qualitative variation was detected and since the number of quantitative variations could be due to chance. For RC, no qualitative variations were observed, but a few spots were significantly variable in protein amount. However, the number of inter-ploidy variations was of the same range as the number of intra-ploidy variations. In conclusion, whatever the ploidy level, leaf and stem proteomes remained globally unchanged in both cabbage lines.
Collapse
Affiliation(s)
- Warren Albertin
- Equipe Génétique Evolutive: Adaptation et Redondance, UMR de Génétique Végétale, INRA/CNRS/UPSud/INAP-G, La Ferme du Moulon, Gif-sur-Yvette, France.
| | | | | | | | | | | | | |
Collapse
|
33
|
Nanto K, Yamada-Watanabe K, Ebinuma H. Agrobacterium-mediated RMCE approach for gene replacement. PLANT BIOTECHNOLOGY JOURNAL 2005; 3:203-14. [PMID: 17173620 DOI: 10.1111/j.1467-7652.2005.00118.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We describe the site-directed integration (SDI) system for Agrobacterium-mediated transformation to precisely integrate a single copy of a desired gene into a predefined target locus by recombinase-mediated cassette exchange (RMCE). The system requires the selection of a transformed line with an integrated copy of a target cassette, and subsequent introduction of an exchange vector. The target cassette contains the npt and cod genes between oppositely orientated recognition sites (RS). The exchange vector T-DNA possesses an exchange cassette containing the gene of interest and a selectable marker gene, such as hpt, between oppositely orientated (inner) RS. Adjacent to the exchange cassette are ipt and recombinase (R) genes and an additional (outer) RS. The recombinase catalyses double-crossover between target RS and exchange inner RS to replace the integrated target cassette with the introduced exchange cassette. Transgenic plants that contain randomly integrated copies of the exchange vector T-DNA show an abnormal phenotype as a result of the overproduction of cytokinin from ipt gene expression. The recombinase can also act on the directly orientated outer RS to remove such randomly integrated copies. The system resulted in single-copy exchange into the target site only in regenerated tobacco at a frequency of 1%-3% per treated explant, or 4%-9% per regenerated line of normal phenotype. Thus, transgenic plants with only an exchanged copy can be efficiently accumulated and selected. Here, we show that the SDI system can efficiently replace the target cassettes with the exchange cassettes in a heterozygous or homozygous condition. The SDI system may be useful for precise comparisons of different gene constructs, the characterization of different chromosomal regions and the cost-effective screening of reliable transgenic plants.
Collapse
Affiliation(s)
- Kazuya Nanto
- Forest Science Laboratory, Nippon Paper Industries Co, Ltd, 5-21-1, Oji, Kita-ku, Tokyo 114-0002, Japan
| | | | | |
Collapse
|
34
|
Pankiewicz R, Karlen Y, Imhof MO, Mermod N. Reversal of the silencing of tetracycline-controlled genes requires the coordinate action of distinctly acting transcription factors. J Gene Med 2005; 7:117-32. [PMID: 15499652 DOI: 10.1002/jgm.644] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Regulation of genes transferred to eukaryotic organisms is often limited by the lack of consistent expression levels in all transduced cells, which may result in part from epigenetic gene silencing effects. This reduces the efficacy of ligand-controlled gene switches designed for somatic gene transfers such as gene therapy. METHODS A doxycycline-controlled transgene was stably introduced in human cells, and clones were screened for epigenetic silencing of the transgene. Various regulatory proteins were targeted to the silent transgene, to identify those that would mediate regulation by doxycycline. RESULTS A doxycycline-controlled minimal promoter was found to be prone to gene silencing, which prevents activation by a fusion of the bacterial TetR DNA-binding domain with the VP16 activator. DNA modification studies indicated that the silenced transgene adopts a poorly accessible chromatin structure. Several cellular transcriptional activators were found to restore an accessible DNA structure when targeted to the silent transgene, and they cooperated with Tet-VP16 to mediate regulation by doxycycline. CONCLUSIONS Reversal of the silencing of a tetracycline-regulated minimal promoter requires a chromatin-remodeling activity for subsequent promoter activation by the Tet-VP16 fusion protein. Thus, distinct regulatory elements may be combined to obtain long-term regulation and persistent expression of exogenous genes in eukaryotic cells.
Collapse
Affiliation(s)
- Renata Pankiewicz
- Laboratory of Molecular Biotechnology, Institute of Biotechnology and Center for Biotechnology UNIL-EPFL, University of Lausanne, 1015 Lausanne, Switzerland
| | | | | | | |
Collapse
|
35
|
Kankainen M, Holm L. POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res 2004; 32:W222-9. [PMID: 15215385 PMCID: PMC441601 DOI: 10.1093/nar/gkh463] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transcription factors can either activate or repress target genes by binding onto short nucleotide sequence motifs in the promoter regions of these genes. Here, we present POBO, a promoter bootstrapping program, for gene expression data. POBO can be used to detect, compare and verify predetermined transcription factor binding site motifs in the promoters of one or two clusters of co-regulated genes. The program calculates the frequencies of the motif in the input promoter sets. A bootstrap analysis detects significantly over- or underrepresented motifs. The output of the program presents bootstrapped results in picture and text formats. The program was tested with published data from transgenic WRKY70 microarray experiments. Intriguingly, motifs recognized by the WRKY transcription factors of plant defense pathways are similarly enriched in both up- and downregulated clusters. POBO analysis suggests slightly modified hypothetical motifs that discriminate between up- and downregulated clusters. In conclusion, POBO allows easy, fast and accurate verification of putative regulatory motifs. The statistical tests implemented in POBO can be useful in eliminating false positives from the results of pattern discovery programs and increasing the reliability of true positives. POBO is freely available from http://ekhidna.biocenter.helsinki.fi:9801/pobo.
Collapse
Affiliation(s)
- Matti Kankainen
- Structural Genomics Group, Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 5), Fin-00014, Helsinki, Finland
| | | |
Collapse
|
36
|
Butaye KMJ, Goderis IJWM, Wouters PFJ, Pues JMTG, Delauré SL, Broekaert WF, Depicker A, Cammue BPA, De Bolle MFC. Stable high-level transgene expression in Arabidopsis thaliana using gene silencing mutants and matrix attachment regions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 39:440-9. [PMID: 15255872 DOI: 10.1111/j.1365-313x.2004.02144.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Basic and applied research involving transgenic plants often requires consistent high-level expression of transgenes. However, high inter-transformant variability of transgene expression caused by various phenomena, including gene silencing, is frequently observed. Here, we show that stable, high-level transgene expression is obtained using Arabidopsis thaliana post-transcriptional gene silencing (PTGS) sgs2 and sgs3 mutants. In populations of first generation (T1) A. thaliana plants transformed with a beta-glucuronidase (GUS) gene (uidA) driven by the 35S cauliflower mosaic virus promoter (p35S), the incidence of highly expressing transformants shifted from 20% in wild type background to 100% in sgs2 and sgs3 backgrounds. Likewise, when sgs2 mutants were transformed with a cyclin-dependent kinase inhibitor 6 gene under control of p35S, all transformants showed a clear phenotype typified by serrated leaves, whereas such phenotype was only observed in about one of five wild type transformants. p35S-driven uidA expression remained high and steady in T2 sgs2 and sgs3 transformants, in marked contrast to the variable expression patterns observed in wild type T2 populations. We further show that T-DNA constructs flanked by matrix attachment regions of the chicken lysozyme gene (chiMARs) cause a boost in GUS activity by fivefold in sgs2 and 12-fold in sgs3 plants, reaching up to 10% of the total soluble proteins, whereas no such boost is observed in the wild type background. MAR-based plant transformation vectors used in a PTGS mutant background might be of high value for efficient high-throughput screening of transgene-based phenotypes as well as for obtaining extremely high transgene expression in plants.
Collapse
Affiliation(s)
- Katleen M J Butaye
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Alami R, Fan Y, Pack S, Sonbuchner TM, Besse A, Lin Q, Greally JM, Skoultchi AI, Bouhassira EE. Mammalian linker-histone subtypes differentially affect gene expression in vivo. Proc Natl Acad Sci U S A 2003; 100:5920-5. [PMID: 12719535 PMCID: PMC156302 DOI: 10.1073/pnas.0736105100] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2002] [Indexed: 01/26/2023] Open
Abstract
Posttranslational modifications and remodeling of nucleosomes are critical factors in the regulation of transcription. Higher-order folding of chromatin also is likely to contribute to the control of gene expression, but the absence of a detailed description of the structure of the chromatin fiber has impaired progress in this area. Mammalian somatic cells contain a set of H1 linker-histone subtypes, H1 (0) and H1a to H1e, that bind to nucleosome core particles and to the linker DNA between nucleosomes. To determine whether the H1 histone subtypes play differential roles in the regulation of gene expression, we combined mice lacking specific H1 histone subtypes with mice carrying transgenes subject to position effects. Because position effects result from the unique chromatin structure created by the juxtaposition of regulatory elements in the transgene and at the site of integration, transgenes can serve as exquisitely sensitive indicators of chromatin structure. We report that some, but not all, linker histones can attenuate or accentuate position effects. The results suggest that the linker-histone subtypes play differential roles in the control of gene expression and that the sequential arrangement of the linker histones on the chromatin fiber might regulate higher-order chromatin structure and fine-tune expression levels.
Collapse
Affiliation(s)
- Raouf Alami
- Department of Medicine, Division of Hematology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Lechtenberg B, Schubert D, Forsbach A, Gils M, Schmidt R. Neither inverted repeat T-DNA configurations nor arrangements of tandemly repeated transgenes are sufficient to trigger transgene silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:507-517. [PMID: 12753589 DOI: 10.1046/j.1365-313x.2003.01746.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Transgene expression was analysed in Arabidopsis T-DNA transformants carrying defined numbers and arrangement of different reporter genes. All transgenes were placed under the control of the strong constitutive CaMV 35S promoter. High, stable transgene expression was observed in plants containing two copies of the beta-glucuronidase (GUS) gene, two or four copies of the green fluorescent protein (GFP) gene and two, four or six copies of the streptomycin phosphotransferase (SPT) gene. Thus, the mere presence of multiple promoter and/or transgene sequences did not result in gene silencing. In none of the cases analysed were tandem repeat arrangements of transgenes and/or inverted repeat (IR) T-DNA structures sufficient to trigger silencing of the different reporter genes. Instead, post-transcriptional gene silencing (PTGS) correlated with the copy number of the highly expressed transgenes. Twelve copies of the SPT and four copies of the GUS gene triggered silencing. Silencing is frequently associated with repetitive T-DNA structures. We favour the idea that in many cases this may be attributed to the high transgene doses rather than the repeat arrangements themselves.
Collapse
Affiliation(s)
- Berthold Lechtenberg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
| | | | | | | | | |
Collapse
|
39
|
Abstract
Gene silencing has evolved in a broad range of organisms probably as defense mechanisms against invasive nucleic acids. Two major strategies are utilized. Transcriptional gene silencing (TGS) acts to prevent RNA synthesis and posttranscriptional gene silencing (PTGS) acts to degrade existing RNA. Although the final effects are similar, the mechanisms of TGS and PTGS are species specific. In most eukaryotes, gene silencing is associated with de novo DNA methylation. However, Caenorhabditis elegans shows an efficient PTGS-like mechanism but lacks a DNA methylation system. Additionally, key enzymes involved in plant and nematode PTGS, the cellular RNA-directed RNA polymerases, appear to be missing in Drosophila melanogaster. In this review, we discuss common features of TGS and PTGS that have been identified across species but for TGS we will concentrate only on methylation-mediated gene inactivation. This effort is complicated by the vague borders between gene silencing and normal gene regulation. Mechanisms that are involved in gene silencing are also used to regulate controlled expression of endogenous genes. To outline the general aspects, gene silencing will be defined as narrowly as possible. The intention behind this review is to stimulate discussion and we seek to facilitate this by introducing speculative concepts that could lead to some reappraisal of the literature.
Collapse
Affiliation(s)
- Michael Wassenegger
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Martinsried, Germany
| |
Collapse
|
40
|
Kim H, Snesrud EC, Haas B, Cheung F, Town CD, Quackenbush J. Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res 2003; 13:327-40. [PMID: 12618363 PMCID: PMC430289 DOI: 10.1101/gr.552003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2002] [Accepted: 12/20/2002] [Indexed: 11/24/2022]
Abstract
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana, we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3' ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region.
Collapse
Affiliation(s)
- Heenam Kim
- The Institute for Genomic Research, Rockville, MD 20850, USA
| | | | | | | | | | | |
Collapse
|
41
|
Gelvin SB. Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol Mol Biol Rev 2003; 67:16-37, table of contents. [PMID: 12626681 PMCID: PMC150518 DOI: 10.1128/mmbr.67.1.16-37.2003] [Citation(s) in RCA: 620] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens and related Agrobacterium species have been known as plant pathogens since the beginning of the 20th century. However, only in the past two decades has the ability of Agrobacterium to transfer DNA to plant cells been harnessed for the purposes of plant genetic engineering. Since the initial reports in the early 1980s using Agrobacterium to generate transgenic plants, scientists have attempted to improve this "natural genetic engineer" for biotechnology purposes. Some of these modifications have resulted in extending the host range of the bacterium to economically important crop species. However, in most instances, major improvements involved alterations in plant tissue culture transformation and regeneration conditions rather than manipulation of bacterial or host genes. Agrobacterium-mediated plant transformation is a highly complex and evolved process involving genetic determinants of both the bacterium and the host plant cell. In this article, I review some of the basic biology concerned with Agrobacterium-mediated genetic transformation. Knowledge of fundamental biological principles embracing both the host and the pathogen have been and will continue to be key to extending the utility of Agrobacterium for genetic engineering purposes.
Collapse
Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
| |
Collapse
|
42
|
Taylor NJ, Fauquet CM. Microparticle bombardment as a tool in plant science and agricultural biotechnology. DNA Cell Biol 2002; 21:963-77. [PMID: 12573053 DOI: 10.1089/104454902762053891] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microparticle bombardment technology has evolved as a method for delivering exogenous nucleic acids into plant cells and is a commonly employed technique in plant science. Desired genetic material is precipitated onto micron-sized metal particles and placed within one of a variety of devices designed to accelerate these "microcarriers" to velocities required to penetrate the plant cell wall. In this manner, transgenes can be delivered into the cell's genome or plastome. Since the late 1980s microparticle bombardment has become a powerful tool for the study of gene expression and production of stably transformed tissues and whole transgenic plants for experimental purposes and agricultural applications. This paper reviews development and application of the technology, including the protocols and mechanical systems employed as delivery systems, and the types of plant cells and culture systems employed to generate effective "targets" for receiving the incoming genetic material. Current understanding of how the exogenous DNA becomes integrated into the plant's native genetic background are assessed as are methods for improving the efficiency of this process. Pros and cons of particle bombardment technologies compared to alternative direct gene transfer methods and Agrobacterium based transformation systems are discussed.
Collapse
Affiliation(s)
- Nigel J Taylor
- International Laboratory for Tropical Agricultural Biotechnology, Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
| | | |
Collapse
|
43
|
Reyes JC, Hennig L, Gruissem W. Chromatin-remodeling and memory factors. New regulators of plant development. PLANT PHYSIOLOGY 2002; 130:1090-101. [PMID: 12427976 PMCID: PMC1540260 DOI: 10.1104/pp.006791] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- José C Reyes
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Isla de la Cartuja, Avenida Américo Vespucio s/n, 41092 Sevilla, Spain
| | | | | |
Collapse
|
44
|
Weber W, Fussenegger M. Artificial mammalian gene regulation networks-novel approaches for gene therapy and bioengineering. J Biotechnol 2002; 98:161-87. [PMID: 12141985 DOI: 10.1016/s0168-1656(02)00130-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Recently developed strategies for targeted molecular interventions in mammalian cells have created novel opportunities in biotechnological and biomedical research with huge economic and therapeutic impact: the design of mammalian cells with desired phenotypes for biopharmaceutical manufacturing, tissue engineering and gene therapy. These advances have been enabled by constructing artificial gene regulation systems with control modalities similar to those evolved in key regulatory networks of mammalian cells. This review highlights recurring cellular regulation strategies and artificial gene regulation technology currently in use for rational reprogramming of cellular key events including metabolism, growth, differentiation and cell death to achieve sophisticated bioprocess and therapeutic goals.
Collapse
Affiliation(s)
- Wilfried Weber
- Institute of Biotechnology, Swiss Federal Institute of Technology, ETH Zurich ETH Hoenggerberg, HPT, Switzerland
| | | |
Collapse
|
45
|
Klöti A, He X, Potrykus I, Hohn T, Fütterer J. Tissue-specific silencing of a transgene in rice. Proc Natl Acad Sci U S A 2002; 99:10881-6. [PMID: 12134059 PMCID: PMC125067 DOI: 10.1073/pnas.152330299] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2001] [Accepted: 06/03/2002] [Indexed: 11/18/2022] Open
Abstract
In a transgenic rice line, a beta-glucuronidase reporter gene under the control of the rice tungro bacilliform virus promoter became gradually methylated, and gene activity was lost concomitantly. Methylation was observed only in the homozygous offspring and was initially restricted to the promoter region and accompanied by loss of expression in the vascular bundle tissue only. This expression pattern was similar to that of a promoter with a deletion of a vascular bundle expression element. The gene activity could be reestablished by treatment with 5-azacytidine. Methylation per se did not inhibit the binding to the promoter region of protein factors which also bound to the unmethylated sequence. Instead, promoter methylation enabled the alternative binding of a protein with specificity for sequence and methylation. In further generations of homozygous offspring the methylation spread into the transcribed region and gene activity was completely repressed also in nonvascular cells. The results indicate that different stages are involved in DNA methylation-correlated gene inactivation, and that at least one of them may involve the attraction of a sequence and methylation-specific DNA-binding protein.
Collapse
Affiliation(s)
- A Klöti
- Institute of Plant Sciences, Federal Institute of Technology, Universitätstrasse 2, CH 8092 Zürich, Switzerland
| | | | | | | | | |
Collapse
|
46
|
Zhang C, Wu-Scharf D, Jeong BR, Cerutti H. A WD40-repeat containing protein, similar to a fungal co-repressor, is required for transcriptional gene silencing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 31:25-36. [PMID: 12100480 DOI: 10.1046/j.1365-313x.2002.01331.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In higher plants, mammals, and filamentous fungi, transcriptional gene silencing is frequently associated with DNA methylation. However, recent evidence suggests that certain transgenes can be inactivated by a methylation independent mechanism. In the unicellular green alga Chlamydomonas reinhardtii, single-copy transgenes are transcriptionally silenced without discernible cytosine methylation of the introduced DNA. We have isolated a Chlamydomonas gene, Mut11, which is required for the transcriptional repression of single-copy transgenes. Mut11 appears to have a global role in gene regulation since it also affects transposon mobilization, cellular growth, and sensitivity to DNA damaging agents. In transient expression assays, a fusion protein between the predicted Mut11 gene product (Mut11p) and E. coli beta-glucuronidase localizes predominantly to the nucleus. Mut11p, a polypeptide of 370 amino acids containing seven WD40 repeats, is highly homologous to proteins of unknown function that are widely distributed among eukaryotes. Mut11p also shows similarity to the C-terminal domain of TUP1, a global transcriptional co-repressor in fungi. Based on these findings we speculate that, in Chlamydomonas, the silencing of certain single-copy transgenes and dispersed transposons integrated into euchromatic regions may occur by a mechanism(s) similar to those involving global transcriptional repressors. Our results also support the existence, in methylation-competent organisms, of a mechanism(s) of transcriptional (trans)gene silencing that is independent of DNA methylation.
Collapse
Affiliation(s)
- Chaomei Zhang
- School of Biological Sciences and Plant Science Initiative, University of Nebraska - Lincoln, E211 Beadle Center, Post Office Box 880666, Lincoln, NE 68588-0666, USA
| | | | | | | |
Collapse
|
47
|
Affiliation(s)
- Peter V Minorsky
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY 10522, USA
| |
Collapse
|
48
|
Affiliation(s)
- Peter V Minorsky
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY 10522, USA.
| |
Collapse
|
49
|
Gaudin V, Libault M, Pouteau S, Juul T, Zhao G, Lefebvre D, Grandjean O. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 2001; 128:4847-58. [PMID: 11731464 DOI: 10.1242/dev.128.23.4847] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In plants, recent studies have demonstrated links between the regulation of developmental processes and chromatin dynamics and organisation. Analysis of new mutations affecting overall plant architecture, leaf development and flowering time in Arabidopsis has allowed us to clone and characterise LHP1, the Drosophila heterochromatin protein 1 (HP1) homologue. LHP1 has the chromo and chromo shadow domains central to the function of animal proteins. Yeast two hybrid studies and in planta deletion experiments suggest similar modes of action in plants and animals via homodimer formation. In vivo localisation experiments revealed a specific subnuclear protein distribution in foci throughout the nucleus. Our data suggest that LHP1 may act as a main regulator of gene expression in plants, through formation of heterochromatin-like repressive complexes, to control developmental pathways involved in organ and cell size, and the vegetative to reproductive phase transition.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Base Sequence
- Cell Nucleus/genetics
- Chromobox Protein Homolog 5
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Cloning, Molecular
- Conserved Sequence
- DNA, Complementary/genetics
- DNA, Plant/genetics
- Dimerization
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genes, Plant
- Molecular Sequence Data
- Mutation
- Plant Leaves/growth & development
- Protein Structure, Tertiary
- Sequence Homology, Amino Acid
Collapse
Affiliation(s)
- V Gaudin
- Laboratoire de Biologie Cellulaire, INRA, route de St Cyr, 78026 Versailles cedex, France.
| | | | | | | | | | | | | |
Collapse
|
50
|
Shen WH. NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2001; 28:371-83. [PMID: 11737775 DOI: 10.1046/j.1365-313x.2001.01135.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The SET- and chromo-domains are recognized as signature motifs for proteins that contribute to epigenetic control of gene expression through effects on the regional organization of chromatin structure. This paper reports the identification of a novel subgroup of SET-domain-containing proteins in tobacco and Arabidopsis, which show highest homologies with the Drosophila position-effect-variegation repressor protein SU(VAR)3-9 and the yeast centromer silencing protein CLR4. The tobacco SET-domain-containing protein (NtSET1) was fused to the green fluorescence protein (GFP) that serves as a visual marker for localization of the recombinant protein in living cells. Whereas control GFP protein alone was uniformly dispersed within the nucleus and cytoplasm, the NtSET1-GFP fusion protein showed a non-uniform localization to multiple nuclear regions in interphase tobacco TBY2 cells. During mitosis, the NtSET1-GFP associated with condensed chromosomes with a non-random distribution. The NtSET1 thus appears to have distinct target regions in the plant chromatin. Overexpression of the NtSET1-GFP in transgenic tobacco inhibited plant growth, implicating the possible involvement of the NtSET1 in transcriptional repression of growth control genes through the formation of higher-order chromatin domains.
Collapse
Affiliation(s)
- W H Shen
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 rue du Général Zimmer, 67084 Strasbourg Cédex, France.
| |
Collapse
|