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Abstract
Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved mechanisms which allow them to adapt to abiotic stresses through alterations in gene expression and metabolism. In recent years, studies have investigated the role of long noncoding RNA (lncRNA) in regulating gene expression in plants and characterized their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications, and RNA-RNA interactions. Genome-wide transcriptome analyses have identified various types of noncoding RNAs (ncRNAs) that respond to abiotic stress. These ncRNAs are in addition to the well-known housekeeping ncRNAs, such as rRNAs, tRNAs, snoRNAs, and snRNAs. In this review, recent research pertaining to the role of lncRNAs in the response of plants to abiotic stress is summarized and discussed.
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan.
- Core Research for Evolutional Science and Technology, Japan Science and Technology, Kawaguchi, Saitama, Japan.
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52
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Diamos AG, Mason HS. Chimeric 3' flanking regions strongly enhance gene expression in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1971-1982. [PMID: 29637682 PMCID: PMC6230951 DOI: 10.1111/pbi.12931] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/07/2018] [Accepted: 03/30/2018] [Indexed: 05/24/2023]
Abstract
Plants represent a promising platform for the highly scalable production of recombinant proteins. Previously, we identified the tobacco extensin terminator lacking its intron as an element that reduced transcript read-through and improved recombinant protein production in a plant-based system. In this study, we systematically compared nonreplicating plant expression vectors containing over 20 commonly used or newly identified terminators from diverse sources. We found that eight gene terminators enhance reporter gene expression significantly more than the commonly used 35S and NOS terminators. The intronless extensin terminator provided a 13.6-fold increase compared with the NOS terminator. Combining terminators in tandem produced large synergistic effects, with many combinations providing a >25-fold increase in expression. Addition of the tobacco Rb7 or TM6 matrix attachment region (MAR) strongly enhanced protein production when added to most terminators, with the Rb7 MAR providing the greatest enhancement. Using deletion analysis, the full activity of the 1193 bp Rb7 MAR was found to require only a 463-bp region at its 3' end. Combined terminators and MAR together provided a >60-fold increase compared with the NOS terminator alone. These combinations were then placed in a replicating geminiviral vector, providing a total of >150-fold enhancement over the original NOS vector, corresponding to an estimated yield of 3-5 g recombinant protein per kg leaf fresh weight or around 50% of the leaf total soluble protein. These results demonstrate the importance of 3' flanking regions in optimizing gene expression and show great potential for 3' flanking regions to improve DNA-based recombinant protein production systems.
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Affiliation(s)
- Andrew G. Diamos
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
| | - Hugh S. Mason
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
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53
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Lee CH, Carroll BJ. Evolution and Diversification of Small RNA Pathways in Flowering Plants. PLANT & CELL PHYSIOLOGY 2018; 59:2169-2187. [PMID: 30169685 DOI: 10.1093/pcp/pcy167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Small regulatory RNAs guide gene silencing at the DNA or RNA level through repression of complementary sequences. The two main forms of small RNAs are microRNA (miRNA) and small interfering RNA (siRNAs), which are generated from the processing of different forms of double-stranded RNA (dsRNA) precursors. These two forms of small regulatory RNAs function in distinct but overlapping gene silencing pathways in plants. Gene silencing pathways in eukaryotes evolved from an ancient prokaryotic mechanism involved in genome defense against invasive genetic elements, but has since diversified to also play a crucial role in regulation of endogenous gene expression. Here, we review the biogenesis of the different forms of small RNAs in plants, including miRNAs, phased, secondary siRNAs (phasiRNAs) and heterochromatic siRNAs (hetsiRNAs), with a focus on their functions in genome defense, transcriptional and post-transcriptional gene silencing, RNA-directed DNA methylation, trans-chromosomal methylation and paramutation. We also discuss the important role that gene duplication has played in the functional diversification of gene silencing pathways in plants, and we highlight recently discovered components of gene silencing pathways in plants.
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Affiliation(s)
- Chin Hong Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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54
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Akasaka M, Taniguchi Y, Oshima M, Abe K, Tabei Y, Tanaka J. Development of transgenic male-sterile rice by using anther-specific promoters identified by comprehensive screening of the gene expression profile database 'RiceXPro'. BREEDING SCIENCE 2018; 68:420-431. [PMID: 30369816 PMCID: PMC6198903 DOI: 10.1270/jsbbs.18019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/24/2018] [Indexed: 05/29/2023]
Abstract
Because genomic selection is designed for the population breeding of allogamous species, a successive outcrossing system is required for efficient use of genomic selection in autogamous crops, such as Oryza sativa L. (rice). Transgenic and dominant male-sterility is a suitable tool for efficient outcrossing of autogamous crops. Though there have been some reports of dominant male-sterile rice developed using transgenic technology, the flowering habit was substandard. Here, to isolate promoters that, when linked to a lethal gene, induce dominant male-sterility while retaining a good flowering habit, we identified 38 candidate genes with anther-specific expression by using the 'RiceXPro' database. We then evaluated the abilities of the near-upstream regions of these genes to induce male-sterility when linked to the lethal gene barnase and introduced into the rice cultivar 'Nipponbare'. Seven of the 38 promoters induced clear dominant male-sterility; promoters expressed in the later stage of anther development induced male-sterility while retaining better flowering habits when compared to ones expressed in the early stage. These seven promoters could potentially be used to facilitate development of an efficient outcross-based breeding system in rice.
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Affiliation(s)
- Maiko Akasaka
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Yojiro Taniguchi
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masao Oshima
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyomi Abe
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yutaka Tabei
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Junichi Tanaka
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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55
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Pérez-González A, Caro E. Effect of transcription terminator usage on the establishment of transgene transcriptional gene silencing. BMC Res Notes 2018; 11:511. [PMID: 30055650 PMCID: PMC6064074 DOI: 10.1186/s13104-018-3649-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
Objective Obtaining high and stable transgene expression is of vital importance for plant genetic engineering. A lot is known about the relationship between terminator efficiency and gene expression, but no studies have addressed the relationship between terminator usage and transgene expression stability or heritable gene silencing. In this paper, we aim to analyze if terminators are a determining factor in the establishment of promoter DNA methylation of plant transgenes. Results Our experiments comparing plants with a LUC reporter under the 35S CaMV promoter and good efficiency terminators (Thsp, T35S) show that the use of efficient terminator sequences does not avoid the accumulation of promoter DNA methylation and transgene silencing. However, Thsp lead to a higher reporter gene expression and lower promoter DNA methylation levels than T35S, supporting that terminator usage is indeed involved in the establishment of TGS by methylation of transgenes’ promoters. In the case of a terminatorless construct, the PTGS initiated by the improperly terminated mRNAs is not followed by the establishment of heritable silencing in the form of strong promoter DNA methylation, like in the case of TAS genes and reactivated TEs (for the transgene DNA methylation levels remained below the 20%). Electronic supplementary material The online version of this article (10.1186/s13104-018-3649-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Pérez-González
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.
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56
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Sheen H, White KA. Expression of T7-based constructs in tobacco cells. Biochem Biophys Res Commun 2018; 499:196-201. [PMID: 29555475 DOI: 10.1016/j.bbrc.2018.03.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
Abstract
Bacteriophage T7 promoter and RNA polymerase (T7-Pol) are widely used for recombinant protein expression in bacteria. In plants, there exists conflicting results regarding the efficacy of protein expression from T7-Pol-derived mRNAs. To reconcile these contradictory observations, the expression of green fluorescent protein (GFP) from T7 constructs was evaluated in tobacco protoplasts. T7 constructs transcribed by a nuclearly targeted T7-Pol did not express GFP in plant protoplasts, however T7-Pol lacking a nuclear targeting signal was able to translate cytosolically transcribed mRNAs, but only if the messages contained a viral translation enhancer. GFP expression was further evaluated at the plant level by using agroinfiltration-mediated transient expression system. Unlike for cytosolic expression, nuclear T7 transcripts containing a viral translation enhancer element did not express GFP, and modifications designed to stabilize and facilitate export of T7 transcripts to the cytosol did not improve the expression. We conclude that expression of nuclear T7 constructs is not feasible in tobacco cells, but cytosolic transcription provides an alternative means to over-express RNAs directly in the cytosol.
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Affiliation(s)
- Hyukho Sheen
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada.
| | - K Andrew White
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada.
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57
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Yamamoto T, Hoshikawa K, Ezura K, Okazawa R, Fujita S, Takaoka M, Mason HS, Ezura H, Miura K. Improvement of the transient expression system for production of recombinant proteins in plants. Sci Rep 2018; 8:4755. [PMID: 29555968 PMCID: PMC5859073 DOI: 10.1038/s41598-018-23024-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/30/2018] [Indexed: 01/24/2023] Open
Abstract
An efficient and high yielding expression system is required to produce recombinant proteins. Furthermore, the transient expression system can be used to identify the localization of proteins in plant cells. In this study, we demonstrated that combination of a geminiviral replication and a double terminator dramatically enhanced the transient protein expression level in plants. The GFP protein was expressed transiently in lettuce, Nicotiana benthamiana, tomatoes, eggplants, hot peppers, melons, and orchids with agroinfiltration. Compared to a single terminator, a double terminator enhanced the expression level. A heat shock protein terminator combined with an extensin terminator resulted in the highest protein expression. Transiently expressed GFP was confirmed by immunoblot analysis with anti-GFP antibodies. Quantitative analysis revealed that the geminiviral vector with a double terminator resulted in the expression of at least 3.7 mg/g fresh weight of GFP in Nicotiana benthamiana, approximately 2-fold that of the geminiviral vector with a single terminator. These results indicated that combination of the geminiviral replication and a double terminator is a useful tool for transient expression of the gene of interest in plant cells.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ken Hoshikawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kentaro Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Risa Okazawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Satoshi Fujita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Miyo Takaoka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hugh S Mason
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute at Arizona State University, Tempe, AZ, 85287, USA
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
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58
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Rosenthal SH, Diamos AG, Mason HS. An intronless form of the tobacco extensin gene terminator strongly enhances transient gene expression in plant leaves. PLANT MOLECULAR BIOLOGY 2018; 96:429-443. [PMID: 29429129 DOI: 10.1007/s11103-018-0708-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 02/01/2018] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE We have found interesting features of a plant gene (extensin) 3' flanking region, including extremely efficient polyadenylation which greatly improves transient expression of transgenes when an intron is removed. Its use will greatly benefit studies of gene expression in plants, research in molecular biology, and applications for recombinant proteins. Plants are a promising platform for the production of recombinant proteins. To express high-value proteins in plants efficiently, the optimization of expression cassettes using appropriate regulatory sequences is critical. Here, we characterize the activity of the tobacco extensin (Ext) gene terminator by transient expression in Nicotiana benthamiana, tobacco, and lettuce. Ext is a member of the hydroxyproline-rich glycoprotein (HRGP) superfamily and constitutes the major protein component of cell walls. The present study demonstrates that the Ext terminator with its native intron removed increased transient gene expression up to 13.5-fold compared to previously established terminators. The enhanced transgene expression was correlated with increased mRNA accumulation and reduced levels of read-through transcripts, which could impair gene expression. Analysis of transcript 3'-ends found that the majority of polyadenylated transcripts were cleaved at a YA dinucleotide downstream from a canonical AAUAAA motif and a UG-rich region, both of which were found to be highly conserved among related extensin terminators. Deletion of either of these regions eliminated most of the activity of the terminator. Additionally, a 45 nt polypurine sequence ~ 175 nt upstream from the polyadenylation sites was found to also be necessary for the enhanced expression. We conclude that the use of Ext terminator has great potential to benefit the production of recombinant proteins in plants.
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Affiliation(s)
- Sun Hee Rosenthal
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Andrew G Diamos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Hugh S Mason
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA.
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59
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Fusaro AF, Barton DA, Nakasugi K, Jackson C, Kalischuk ML, Kawchuk LM, Vaslin MFS, Correa RL, Waterhouse PM. The Luteovirus P4 Movement Protein Is a Suppressor of Systemic RNA Silencing. Viruses 2017; 9:v9100294. [PMID: 28994713 PMCID: PMC5691645 DOI: 10.3390/v9100294] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 11/16/2022] Open
Abstract
The plant viral family Luteoviridae is divided into three genera: Luteovirus, Polerovirus and Enamovirus. Without assistance from another virus, members of the family are confined to the cells of the host plant's vascular system. The first open reading frame (ORF) of poleroviruses and enamoviruses encodes P0 proteins which act as silencing suppressor proteins (VSRs) against the plant's viral defense-mediating RNA silencing machinery. Luteoviruses, such as barley yellow dwarf virus-PAV (BYDV-PAV), however, have no P0 to carry out the VSR role, so we investigated whether other proteins or RNAs encoded by BYDV-PAV confer protection against the plant's silencing machinery. Deep-sequencing of small RNAs from plants infected with BYDV-PAV revealed that the virus is subjected to RNA silencing in the phloem tissues and there was no evidence of protection afforded by a possible decoy effect of the highly abundant subgenomic RNA3. However, analysis of VSR activity among the BYDV-PAV ORFs revealed systemic silencing suppression by the P4 movement protein, and a similar, but weaker, activity by P6. The closely related BYDV-PAS P4, but not the polerovirus potato leafroll virus P4, also displayed systemic VSR activity. Both luteovirus and the polerovirus P4 proteins also showed transient, weak local silencing suppression. This suggests that systemic silencing suppression is the principal mechanism by which the luteoviruses BYDV-PAV and BYDV-PAS minimize the effects of the plant's anti-viral defense.
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Affiliation(s)
- Adriana F Fusaro
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- Plant Industry Division, CSIRO, P.O. Box 1600, Canberra, ACT 2601, Australia.
- Department of Virology (M.F.S.V.), Department of Genetics (R.L.C.) and Institute of Medical Biochemistry (A.F.F.), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil.
| | - Deborah A Barton
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Kenlee Nakasugi
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Craig Jackson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Melanie L Kalischuk
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA.
| | - Lawrence M Kawchuk
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- Department of Agriculture and Agri-Food Canada, Lethbridge, AB T1J4B1, Canada.
| | - Maite F S Vaslin
- Department of Virology (M.F.S.V.), Department of Genetics (R.L.C.) and Institute of Medical Biochemistry (A.F.F.), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil.
| | - Regis L Correa
- Plant Industry Division, CSIRO, P.O. Box 1600, Canberra, ACT 2601, Australia.
- Department of Virology (M.F.S.V.), Department of Genetics (R.L.C.) and Institute of Medical Biochemistry (A.F.F.), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil.
| | - Peter M Waterhouse
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- Plant Industry Division, CSIRO, P.O. Box 1600, Canberra, ACT 2601, Australia.
- School of Earth, Environmental and Biological sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia.
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60
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Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis. THE PLANT CELL 2017; 29:1836-1863. [PMID: 28705956 PMCID: PMC5590493 DOI: 10.1105/tpc.16.00828] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 06/22/2017] [Accepted: 07/11/2017] [Indexed: 05/19/2023]
Abstract
Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5'-3' RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.
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Affiliation(s)
- Peter A Crisp
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Aaron B Smith
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Kevin D Murray
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Gonzalo M Estavillo
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- CSIRO Agriculture and Food, Black Mountain, Canberra ACT 2601, Australia
| | - Iain Searle
- School of Biological Sciences, The University of Adelaide, SA 5005, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
| | - Ozren Bogdanović
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
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Tyč D, Nocarová E, Sikorová L, Fischer L. 5-Azacytidine mediated reactivation of silenced transgenes in potato (Solanum tuberosum) at the whole plant level. PLANT CELL REPORTS 2017; 36:1311-1322. [PMID: 28510781 DOI: 10.1007/s00299-017-2155-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
Transient 5-azacytidine treatment of leaf explants from potato plants with transcriptionally silenced transgenes allows de novo regeneration of plants with restored transgene expression at the whole plant level. Transgenes introduced into plant genomes frequently become silenced either at the transcriptional or the posttranscriptional level. Transcriptional silencing is usually associated with DNA methylation in the promoter region. Treatments with inhibitors of maintenance DNA methylation were previously shown to allow reactivation of transcriptionally silenced transgenes in single cells or tissues, but not at the whole plant level. Here we analyzed the effect of DNA methylation inhibitor 5-azacytidine (AzaC) on the expression of two silenced reporter genes encoding green fluorescent protein (GFP) and neomycin phosphotransferase (NPTII) in potato plants. Whereas no obvious reactivation was observed in AzaC-treated stem cuttings, transient treatment of leaf segments with 10 μM AzaC and subsequent de novo regeneration of shoots on the selective medium with kanamycin resulted in the production of whole plants with clearly reactivated expression of previously silenced transgenes. Reactivation of nptII expression was accompanied by a decrease in cytosine methylation in the promoter region of the gene. Using the plants with reactivated GFP expression, we found that re-silencing of this transgene can be accidentally triggered by de novo regeneration. Thus, testing the incidence of transgene silencing during de novo regeneration could be a suitable procedure for negative selection of transgenic lines (insertion events) which have an inclination to be silenced. Based on our analysis of non-specific inhibitory effects of AzaC on growth of potato shoots in vitro, we estimated that AzaC half-life in the culture media is approximately 2 days.
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Affiliation(s)
- Dimitrij Tyč
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Vinicna 5, CZ 128 44, Prague 2, Czech Republic
| | - Eva Nocarová
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Vinicna 5, CZ 128 44, Prague 2, Czech Republic
| | - Lenka Sikorová
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Vinicna 5, CZ 128 44, Prague 2, Czech Republic
| | - Lukáš Fischer
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Vinicna 5, CZ 128 44, Prague 2, Czech Republic.
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Abstract
RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in Neurospora crassa, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom. However, an increasing number of fungal sRNAs with regulatory functions generated by specific RNAi pathways have been identified. Several mechanistic aspects of the biogenesis of these sRNAs are known, but their function in fungal development and physiology is scarce, except for remarkable examples such as Mucor circinelloides, in which specific sRNAs clearly regulate responses to environmental and endogenous signals. Despite the retention of RNAi in most species, some fungal groups and species lack an active RNAi mechanism, suggesting that its loss may provide some selective advantage. This article summarizes the current understanding of RNAi functions in the fungal kingdom.
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63
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Torres-Martínez S, Ruiz-Vázquez RM. The RNAi Universe in Fungi: A Varied Landscape of Small RNAs and Biological Functions. Annu Rev Microbiol 2017; 71:371-391. [PMID: 28657888 DOI: 10.1146/annurev-micro-090816-093352] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is a conserved eukaryotic mechanism that uses small RNA molecules to suppress gene expression through sequence-specific messenger RNA degradation, translational repression, or transcriptional inhibition. In filamentous fungi, the protective function of RNAi in the maintenance of genome integrity is well known. However, knowledge of the regulatory role of RNAi in fungi has had to wait until the recent identification of different endogenous small RNA classes, which are generated by distinct RNAi pathways. In addition, RNAi research on new fungal models has uncovered the role of small RNAs and RNAi pathways in the regulation of diverse biological functions. In this review, we give an up-to-date overview of the different classes of small RNAs and RNAi pathways in fungi and their roles in the defense of genome integrity and regulation of fungal physiology and development, as well as in the interaction of fungi with biotic and abiotic environments.
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64
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Effect of gene order in DNA constructs on gene expression upon integration into plant genome. 3 Biotech 2017; 7:94. [PMID: 28555430 DOI: 10.1007/s13205-017-0729-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/29/2017] [Indexed: 10/19/2022] Open
Abstract
Several plant biotechnology applications are based on the expression of multiple genes located on a single transformation vector. The principles of stable expression of foreign genes in plant cells include integration of full-length gene fragments consisting of promoter and transcription terminator sequences, and avoiding converging orientation of the gene transcriptional direction. Therefore, investigators usually generate constructs in which genes are assembled in the same orientation. However, no specific information is available on the effect of the order in which genes should be assembled in the construct to support optimum expression of each gene upon integration in the genome. While many factors, including genomic position and the integration structure, could affect gene expression, the investigators judiciously design DNA constructs to avoid glitches. However, the gene order in a multigene assembly remains an open question. This study addressed the effect of gene order in the DNA construct on gene expression in rice using a simple design of two genes placed in two possible orders with respect to the genomic context. Transgenic rice lines containing green fluorescent protein (GFP) and β-glucuronidase (GUS) genes in two distinct orders were developed by Cre-lox-mediated site-specific integration. Gene expression analysis of transgenic lines showed that both genes were expressed at similar levels in either orientation, and different transgenic lines expressed each gene within 1-2× range. Thus, no significant effect of the gene order on gene expression was found in the transformed rice lines containing precise site-specific integrations and stable gene expression in plant cells could be obtained with altered gene orders. Therefore, gene orientation and integration structures are more important factors governing gene expression than gene orders in the genomic context.
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Baeg K, Iwakawa HO, Tomari Y. The poly(A) tail blocks RDR6 from converting self mRNAs into substrates for gene silencing. NATURE PLANTS 2017; 3:17036. [PMID: 28319057 DOI: 10.1038/nplants.2017.36] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/19/2017] [Indexed: 05/20/2023]
Abstract
It remains unclear how post-transcriptional gene silencing (PTGS) in plants discriminates aberrant RNAs from canonical messenger RNAs (mRNAs). The key step of plant PTGS is the conversion of aberrant RNAs into double-stranded RNAs by RNA-DEPENDENT RNA POLYMERASE6 (RDR6). Here, we show that RDR6 itself selects aberrant poly(A)-less mRNAs over canonical polyadenylated mRNAs as templates at the initiation step of complementary strand synthesis. This mechanism can be viewed as an innate safeguard against 'self-attack' by PTGS.
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Affiliation(s)
- Kyungmin Baeg
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiro-Oki Iwakawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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66
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Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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67
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Conti G, Zavallo D, Venturuzzi AL, Rodriguez MC, Crespi M, Asurmendi S. TMV induces RNA decay pathways to modulate gene silencing and disease symptoms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:73-84. [PMID: 27599263 DOI: 10.1111/tpj.13323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/23/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
RNA decay pathways comprise a combination of RNA degradation mechanisms that are implicated in gene expression, development and defense responses in eukaryotes. These mechanisms are known as the RNA Quality Control or RQC pathways. In plants, another important RNA degradation mechanism is the post-transcriptional gene silencing (PTGS) mediated by small RNAs (siRNAs). Notably, the RQC pathway antagonizes PTGS by preventing the entry of dysfunctional mRNAs into the silencing pathway to avoid global degradation of mRNA by siRNAs. Viral transcripts must evade RNA degrading mechanisms, thus viruses encode PTGS suppressor proteins to counteract viral RNA silencing. Here, we demonstrate that tobacco plants infected with TMV and transgenic lines expressing TMV MP and CP (coat protein) proteins (which are not linked to the suppression of silencing) display increased transcriptional levels of RNA decay genes. These plants also showed accumulation of cytoplasmic RNA granules with altered structure, increased rates of RNA decay for transgenes and defective transgene PTGS amplification. Furthermore, knockdown of RRP41 or RRP43 RNA exosome components led to lower levels of TMV accumulation with milder symptoms after infection, several developmental defects and miRNA deregulation. Thus, we propose that TMV proteins induce RNA decay pathways (in particular exosome components) to impair antiviral PTGS and this defensive mechanism would constitute an additional counter-defense strategy that lead to disease symptoms.
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Affiliation(s)
- Gabriela Conti
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Andrea L Venturuzzi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
| | | | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, IPS2, CNRS, INRA, University Paris-Sud, Orsay, France
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
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68
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Liu L, Yan X, Kong X, Zhao Y, Gong Z, Jin JB, Guo Y. Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway. PLANT PHYSIOLOGY 2017; 173:655-667. [PMID: 27852949 PMCID: PMC5210737 DOI: 10.1104/pp.16.01365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/14/2016] [Indexed: 05/21/2023]
Abstract
The expression of genes with aberrant structure is prevented at both the transcriptional and posttranscriptional regulation levels. Aberrant gene silencing at the posttranscriptional level is well studied; however, it is not well understood how aberrant genes are silenced at the transcriptional level. In this study, through genetic screening a transgenic report line that harbors an aberrant gene (35S-LUC, lacking 3'-untranslated region [3'-UTR]) and lacks luciferase (LUC) activity, we identify that the small ubiquitin-like modifier (SUMO) protease OTS1 gene is required for maintaining the silence of the reporter 35S-LUC and an endogenous mutator-like element MULE-F19G14 at the transcriptional level, which requires DNA-dependent RNA polymerase (Pol) V and DDR complex, but not Pol IV. The increased transcripts in ots1 mutants are terminated by the 3'-UTRs of downstream genes. In addition to ots1 mutations, mutations in several known or putative SUMO proteases and two SUMO E3 ligases, SIZ1 and MMS21, have similar effects on this silencing regulation. Taken together, our results reveal that the enzymes involved in the SUMOylation process restrain aberrant gene transcription by using a downstream gene 3'-UTR, and this regulation requires a functional Pol V-dependent pathway in Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Xiaojing Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Xiangxiong Kong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Yiqiang Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Jing Bo Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
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69
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Zhou Y, Yang Y, Zhou X, Chi Y, Fan B, Chen Z. Structural and Functional Characterization of the VQ Protein Family and VQ Protein Variants from Soybean. Sci Rep 2016; 6:34663. [PMID: 27708406 PMCID: PMC5052590 DOI: 10.1038/srep34663] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/13/2016] [Indexed: 11/09/2022] Open
Abstract
Proteins containing the FxxxVQxhTG or VQ motif interact with WRKY transcription factors. Although VQ proteins have been reported in several plants, knowledge about their structures, functions and evolution is still very limited. Here, we report structural and functional analysis of the VQ protein family from soybean. Like Arabidopsis homologues, soybean VQ proteins bind only Group I and IIc WRKY proteins and a substantial number of their genes are responsive to stress-associated phytohormones. Overexpression of some soybean VQ genes in Arabidopsis had strong effects on plant growth, development, disease resistance and heat tolerance. Phylogenetic analysis, sequence alignment and site-directed mutagenesis revealed that the region immediately upstream of the FxxxVQxhTG motif also affects binding to WRKY proteins. Consistent with a larger WRKY-binding VQ domain, soybean VQ22 protein from cultivated soybean contains a 4-amino acid deletion in the region preceding its VQ motif that completely abolishes its binding to WRKY proteins. By contrast, the 4-amino acid deletion is absent in the VQ22 protein from wild soybean species (Glycine soja). Overexpression of wild soybean VQ22 in cultivated soybean inhibited growth, particularly after cold treatment. Thus, the mutation of soybean VQ22 is associated with advantageous phenotypes and may have been positively selected during evolution.
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Affiliation(s)
- Yuan Zhou
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Xinjian Zhou
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yingjun Chi
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Baofang Fan
- Department of Botany and Plant Pathology, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
- Department of Botany and Plant Pathology, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA
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70
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DNA methylation signature of intergenic region involves in nucleosome remodeler DDM1-mediated repression of aberrant gene transcriptional read-through. J Genet Genomics 2016; 43:513-23. [DOI: 10.1016/j.jgg.2016.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/23/2022]
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71
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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72
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Kubota K, Ng JCK. Lettuce chlorosis virus P23 Suppresses RNA Silencing and Induces Local Necrosis with Increased Severity at Raised Temperatures. PHYTOPATHOLOGY 2016; 106:653-62. [PMID: 26828232 DOI: 10.1094/phyto-09-15-0219-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RNA silencing functions as an antivirus defense strategy in plants, one that plant viruses counter by producing viral suppressors of RNA silencing (VSRs). VSRs have been identified in three members of the genus Crinivirus but they do not all share identical suppression mechanisms. Here, we used Agrobacterium co-infiltration assays to investigate the suppressor activity of proteins encoded by Lettuce chlorosis virus (LCV). Of 7 LCV proteins (1b, P23, HSP70 homolog, P60, CP, CPm, and P27) tested for the suppression of silencing of green fluorescent protein (GFP) expression in wild-type Nicotiana benthamiana plants, only P23 suppressed the onset of local silencing. Small-interfering (si)RNA accumulation was reduced in leaves co-infiltrated with P23, suggesting that P23 inhibited the accumulation or enhanced the degradation of siRNA. P23 also inhibited the cell-to-cell and systemic movement of RNA silencing in GFP-expressing transgenic N. benthamiana plants. Expression of P23 via agroinfiltration of N. benthamiana leaves induced local necrosis that increased in severity at elevated temperatures, a novelty given that a direct temperature effect on necrosis severity has not been reported for the other crinivirus VSRs. These results further affirm the sophistication of crinivirus VSRs in mediating the evasion of host's antiviral defenses and in symptom modulation.
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Affiliation(s)
- Kenji Kubota
- First author: NARO Agricultural Research Center, Kannondai, Tsukuba, Ibaraki 305-8666, Japan, and Department of Plant Pathology and Microbiology, University of California, Riverside 92521; second author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521
| | - James C K Ng
- First author: NARO Agricultural Research Center, Kannondai, Tsukuba, Ibaraki 305-8666, Japan, and Department of Plant Pathology and Microbiology, University of California, Riverside 92521; second author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521
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73
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Garcia-Ruiz H, Ruiz MTG, Peralta SMG, Gabriel CBM, El-Mounadi K. Mechanisms, applications, and perspectives of antiviral RNA silencing in plants. ACTA ACUST UNITED AC 2016; 34. [PMID: 28890589 DOI: 10.18781/r.mex.fit.1606-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Viral diseases of plants cause important economic losses due to reduction in crop quality and quantity to the point of threatening food security in some countries. Given the reduced availability of natural sources, genetic resistance to viruses has been successfully engineered for some plant-virus combinations. A sound understanding of the basic mechanisms governing plant-virus interactions, including antiviral RNA silencing, is the foundation to design better management strategies and biotechnological approaches to engineer and implement antiviral resistance in plants. In this review, we present current molecular models to explain antiviral RNA silencing and its application in basic plant research, biotechnology and genetic engineering.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | | | | | | | - Kautar El-Mounadi
- Department of Biology, Kuztown University of Pennsylvania, Kuztown, PA 19530 USA
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74
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Goto S, Sasakura-Shimoda F, Yamazaki M, Hayashi N, Suetsugu M, Ochiai H, Takatsuji H. Development of disease-resistant rice by pathogen-responsive expression of WRKY45. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1127-38. [PMID: 26448265 DOI: 10.1111/pbi.12481] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/20/2015] [Accepted: 08/28/2015] [Indexed: 05/28/2023]
Abstract
WRKY45 is an important transcription factor in the salicylic acid signalling pathway in rice that mediates chemical-induced resistance against multiple pathogens. Its constitutive overexpression confers extremely strong resistance against Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae to rice, but has adverse effects on agronomic traits. Here, a new strategy to confer rice with strong disease resistance without any negative effects on agronomic traits was established by expressing WRKY45 under the control of pathogen-responsive promoters in combination with a translational enhancer derived from a 5'-untranslated region (UTR) of rice alcohol dehydrogenase (ADH). Rice promoters that responded to M. oryzae and X. oryzae pv. oryzae infections within 24 h were identified, and 2-kb upstream sequences from nine of them were isolated, fused to WRKY45 cDNA with or without the ADH 5'-UTR, and introduced into rice. Although pathogen-responsive promoters alone failed to confer effective disease resistance, the use of the ADH 5'-UTR in combination with them, in particular the PR1b and GST promoters, enhanced disease resistance. Field trials showed that overall, PR1b promoter-driven (with ADH 5'-UTR) lines performed the best and one had agronomic traits comparable to control untransformed rice. Thus, expressing WRKY45 under the control of the PR1b promoter with the ADH 5'-UTR is an excellent strategy to develop disease-resistant rice, and the line established could serve as a mother line for breeding disease-resistant rice.
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Affiliation(s)
- Shingo Goto
- Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Fuyuko Sasakura-Shimoda
- Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Muneo Yamazaki
- Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Nagao Hayashi
- Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Mai Suetsugu
- Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hirokazu Ochiai
- Plant-Microbe Interaction Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Hiroshi Takatsuji
- Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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75
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Diamos AG, Rosenthal SH, Mason HS. 5' and 3' Untranslated Regions Strongly Enhance Performance of Geminiviral Replicons in Nicotiana benthamiana Leaves. FRONTIERS IN PLANT SCIENCE 2016; 7:200. [PMID: 26941764 PMCID: PMC4764687 DOI: 10.3389/fpls.2016.00200] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/05/2016] [Indexed: 05/24/2023]
Abstract
We previously reported a recombinant protein production system based on a geminivirus replicon that yields high levels of vaccine antigens and monoclonal antibodies in plants. The bean yellow dwarf virus (BeYDV) replicon generates massive amounts of DNA copies, which engage the plant transcription machinery. However, we noticed a disparity between transcript level and protein production, suggesting that mRNAs could be more efficiently utilized. In this study, we systematically evaluated genetic elements from human, viral, and plant sources for their potential to improve the BeYDV system. The tobacco extensin terminator enhanced transcript accumulation and protein production compared to other commonly used terminators, indicating that efficient transcript processing plays an important role in recombinant protein production. Evaluation of human-derived 5' untranslated regions (UTRs) indicated that many provided high levels of protein production, supporting their cross-kingdom function. Among the viral 5' UTRs tested, we found the greatest enhancement with the tobacco mosaic virus omega leader. An analysis of the 5' UTRs from the Arabidopsis thaliana and Nicotinana benthamiana photosystem I K genes found that they were highly active when truncated to include only the near upstream region, providing a dramatic enhancement of transgene production that exceeded that of the tobacco mosaic virus omega leader. The tobacco Rb7 matrix attachment region inserted downstream from the gene of interest provided significant enhancement, which was correlated with a reduction in plant cell death. Evaluation of Agrobacterium strains found that EHA105 enhanced protein production and reduced cell death compared to LBA4301 and GV3101. We used these improvements to produce Norwalk virus capsid protein at >20% total soluble protein, corresponding to 1.8 mg/g leaf fresh weight, more than twice the highest level ever reported in a plant system. We also produced the monoclonal antibody rituximab at 1 mg/g leaf fresh weight.
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76
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Qian X, Hamid FM, El Sahili A, Darwis DA, Wong YH, Bhushan S, Makeyev EV, Lescar J. Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases. J Biol Chem 2016; 291:9295-309. [PMID: 26907693 PMCID: PMC4861493 DOI: 10.1074/jbc.m115.685933] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/15/2022] Open
Abstract
Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1(Ncr)) and related fungi, Thielavia terrestris (QDE-1(Tte)) and Myceliophthora thermophila (QDE-1(Mth)), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1(Ncr) counterpart favoring processive RNA synthesis, QDE-1(Tte) and QDE-1(Mth) produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1(Tte) reveals a quasisymmetric dimer similar to QDE-1(Ncr) Further electron microscopy analyses confirm that QDE-1(Tte) occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure.
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Affiliation(s)
- Xinlei Qian
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Fursham M Hamid
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Abbas El Sahili
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Dina Amallia Darwis
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Yee Hwa Wong
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Shashi Bhushan
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Eugene V Makeyev
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, the Medical Research Council Centre for Developmental Neurobiology, King's College, London SE1 1UL, United Kingdom, and
| | - Julien Lescar
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, UPMC UMRS CR7-CNRS ERL 8255-INSERM U1135 Centre d' Immunologie et des Maladies Infectieuses, Faculté de Médecine Pierre et Marie Curie, Centre Hospitalier Universitaire Pitié-Salpêtrière, 75031 Paris, France
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77
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Crisp PA, Ganguly D, Eichten SR, Borevitz JO, Pogson BJ. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics. SCIENCE ADVANCES 2016; 2:e1501340. [PMID: 26989783 PMCID: PMC4788475 DOI: 10.1126/sciadv.1501340] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/08/2015] [Indexed: 05/18/2023]
Abstract
Plants grow in dynamic environments where they can be exposed to a multitude of stressful factors, all of which affect their development, yield, and, ultimately, reproductive success. Plants are adept at rapidly acclimating to stressful conditions and are able to further fortify their defenses by retaining memories of stress to enable stronger or more rapid responses should an environmental perturbation recur. Indeed, one mechanism that is often evoked regarding environmental memories is epigenetics. Yet, there are relatively few examples of such memories; neither is there a clear understanding of their duration, considering the plethora of stresses in nature. We propose that this field would benefit from investigations into the processes and mechanisms enabling recovery from stress. An understanding of stress recovery could provide fresh insights into when, how, and why environmental memories are created and regulated. Stress memories may be maladaptive, hindering recovery and affecting development and potential yield. In some circumstances, it may be advantageous for plants to learn to forget. Accordingly, the recovery process entails a balancing act between resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting the epigenome and transcriptome and in altering memory. Exploration of this emerging area of research is becoming ever more tractable with advances in genomics, phenomics, and high-throughput sequencing methodology that will enable unprecedented profiling of high-resolution stress recovery time series experiments and sampling of large natural populations.
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78
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Branscheid A, Marchais A, Schott G, Lange H, Gagliardi D, Andersen SU, Voinnet O, Brodersen P. SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Nucleic Acids Res 2015; 43:10975-88. [PMID: 26464441 PMCID: PMC4678812 DOI: 10.1093/nar/gkv1014] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022] Open
Abstract
Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20–24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5′, but not 3′-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5′ to the cleavage site, but several examples of 3′-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5′-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5′-cleavage fragments.
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Affiliation(s)
- Anja Branscheid
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Antonin Marchais
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Gregory Schott
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Heike Lange
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Olivier Voinnet
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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79
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Yu A, Saudemont B, Bouteiller N, Elvira-Matelot E, Lepère G, Parent JS, Morel JB, Cao J, Elmayan T, Vaucheret H. Second-Site Mutagenesis of a Hypomorphic argonaute1 Allele Identifies SUPERKILLER3 as an Endogenous Suppressor of Transgene Posttranscriptional Gene Silencing. PLANT PHYSIOLOGY 2015; 169:1266-74. [PMID: 26286717 PMCID: PMC4587451 DOI: 10.1104/pp.15.00585] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/16/2015] [Indexed: 05/21/2023]
Abstract
Second-site mutagenesis was performed on the argonaute1-33 (ago1-33) hypomorphic mutant, which exhibits reduced sense transgene posttranscriptional gene silencing (S-PTGS). Mutations in FIERY1, a positive regulator of the cytoplasmic 5'-to-3' EXORIBONUCLEASE4 (XRN4), and in SUPERKILLER3 (SKI3), a member of the SKI complex that threads RNAs directly to the 3'-to-5' exoribonuclease of the cytoplasmic exosome, compensated AGO1 partial deficiency and restored S-PTGS with 100% efficiency. Moreover, xrn4 and ski3 single mutations provoked the entry of nonsilenced transgenes into S-PTGS and enhanced S-PTGS on partially silenced transgenes, indicating that cytoplasmic 5'-to-3' and 3'-to-5' RNA degradation generally counteract S-PTGS, likely by reducing the amount of transgene aberrant RNAs that are used by the S-PTGS pathway to build up small interfering RNAs that guide transgene RNA cleavage by AGO1. Constructs generating improperly terminated transgene messenger RNAs (mRNAs) were not more sensitive to ski3 or xrn4 than regular constructs, suggesting that improperly terminated transgene mRNAs not only are degraded from both the 3' end but also from the 5' end, likely after decapping. The facts that impairment of either 5'-to-3' or 3'-to-5' RNA degradation is sufficient to provoke the entry of transgene RNA into the S-PTGS pathway, whereas simultaneous impairment of both pathways is necessary to provoke the entry of endogenous mRNA into the S-PTGS pathway, suggest poor RNA quality upon the transcription of transgenes integrated at random genomic locations.
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Affiliation(s)
- Agnès Yu
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Baptiste Saudemont
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Emilie Elvira-Matelot
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Gersende Lepère
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Jean-Sébastien Parent
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Jean-Benoit Morel
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Jun Cao
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Taline Elmayan
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique (INRA), 78000 Versailles, France (A.Y., B.S., N.B., E.E.-M., G.L., J.-S.P., J.-B.M., T.E., H.V.); andDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany (J.C.)
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80
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Dalakouras A, Dadami E, Wassenegger M. Viroid-induced DNA methylation in plants. Biomol Concepts 2015; 4:557-65. [PMID: 25436756 DOI: 10.1515/bmc-2013-0030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/26/2013] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). RdDM was first discovered in viroid-infected plants. Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. Here, we provide an overview of the cumulative data on the field of viroid-induced RdDM and discuss three possible scenarios concerning the mechanistic details of its establishment.
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81
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Parent JS, Jauvion V, Bouché N, Béclin C, Hachet M, Zytnicki M, Vaucheret H. Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes. Nucleic Acids Res 2015. [PMID: 26209135 PMCID: PMC4787800 DOI: 10.1093/nar/gkv753] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although post-transcriptional gene silencing (PTGS) has been studied for more than a decade, there is still a gap in our understanding of how de novo silencing is initiated against genetic elements that are not supposed to produce double-stranded (ds)RNA. Given the pervasive transcription occurring throughout eukaryote genomes, we tested the hypothesis that unintended transcription could produce antisense (as)RNA molecules that participate to the initiation of PTGS triggered by sense transgenes (S-PTGS). Our results reveal a higher level of asRNA in Arabidopsis thaliana lines that spontaneously trigger S-PTGS than in lines that do not. However, PTGS triggered by antisense transgenes (AS-PTGS) differs from S-PTGS. In particular, a hypomorphic ago1 mutation that suppresses S-PTGS prevents the degradation of asRNA but not sense RNA during AS-PTGS, suggesting a different treatment of coding and non-coding RNA by AGO1, likely because of AGO1 association to polysomes. Moreover, the intended asRNA produced during AS-PTGS is capped whereas the asRNA produced during S-PTGS derives from 3′ maturation of a read-through transcript and is uncapped. Thus, we propose that uncapped asRNA corresponds to the aberrant RNA molecule that is converted to dsRNA by RNA-DEPENDENT RNA POLYMERASE 6 in siRNA-bodies to initiate S-PTGS, whereas capped asRNA must anneal with sense RNA to produce dsRNA that initiate AS-PTGS.
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Affiliation(s)
| | - Vincent Jauvion
- Institut Jean-Pierre Bourgin, UMR1318, INRA, 78000 Versailles, France
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, UMR1318, INRA, 78000 Versailles, France
| | - Christophe Béclin
- Institut Jean-Pierre Bourgin, UMR1318, INRA, 78000 Versailles, France
| | | | | | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR1318, INRA, 78000 Versailles, France
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82
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Foresi N, Mayta ML, Lodeyro AF, Scuffi D, Correa-Aragunde N, García-Mata C, Casalongué C, Carrillo N, Lamattina L. Expression of the tetrahydrofolate-dependent nitric oxide synthase from the green alga Ostreococcus tauri increases tolerance to abiotic stresses and influences stomatal development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:806-21. [PMID: 25880454 DOI: 10.1111/tpj.12852] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 03/17/2015] [Accepted: 04/01/2015] [Indexed: 05/17/2023]
Abstract
Nitric oxide (NO) is a signaling molecule with diverse biological functions in plants. NO plays a crucial role in growth and development, from germination to senescence, and is also involved in plant responses to biotic and abiotic stresses. In animals, NO is synthesized by well-described nitric oxide synthase (NOS) enzymes. NOS activity has also been detected in higher plants, but no gene encoding an NOS protein, or the enzymes required for synthesis of tetrahydrobiopterin, an essential cofactor of mammalian NOS activity, have been identified so far. Recently, an NOS gene from the unicellular marine alga Ostreococcus tauri (OtNOS) has been discovered and characterized. Arabidopsis thaliana plants were transformed with OtNOS under the control of the inducible short promoter fragment (SPF) of the sunflower (Helianthus annuus) Hahb-4 gene, which responds to abiotic stresses and abscisic acid. Transgenic plants expressing OtNOS accumulated higher NO concentrations compared with siblings transformed with the empty vector, and displayed enhanced salt, drought and oxidative stress tolerance. Moreover, transgenic OtNOS lines exhibited increased stomatal development compared with plants transformed with the empty vector. Both in vitro and in vivo experiments indicate that OtNOS, unlike mammalian NOS, efficiently uses tetrahydrofolate as a cofactor in Arabidopsis plants. The modulation of NO production to alleviate abiotic stress disturbances in higher plants highlights the potential of genetic manipulation to influence NO metabolism as a tool to improve plant fitness under adverse growth conditions.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Martín L Mayta
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Anabella F Lodeyro
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Denise Scuffi
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Carlos García-Mata
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Claudia Casalongué
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
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83
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Trieu TA, Calo S, Nicolás FE, Vila A, Moxon S, Dalmay T, Torres-Martínez S, Garre V, Ruiz-Vázquez RM. A non-canonical RNA silencing pathway promotes mRNA degradation in basal Fungi. PLoS Genet 2015; 11:e1005168. [PMID: 25875805 PMCID: PMC4395119 DOI: 10.1371/journal.pgen.1005168] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/20/2015] [Indexed: 12/04/2022] Open
Abstract
The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing. Most eukaryotic organisms produce different classes of endogenous small RNA (esRNA) molecules that suppress gene expression through RNA interference (RNAi) pathways. These pathways, which may differ among organisms, are normally involved in genome defense, heterochromatin formation and regulation of genes involved in multiple cellular functions. In the basal fungus Mucor circinelloides, an opportunistic human pathogen, we previously demonstrated that biogenesis of a large group of esRNA molecules requires a basic RNAi machinery consisting of a Dicer-like protein, an Argonaute nuclease and two RNA-dependent RNA polymerases. This canonical dicer-dependent pathway regulates different cellular processes, such as vegetative sporulation. Besides those esRNAs generated by this canonical RNAi pathway, we have identified a new rdrp-dependent dicer-independent esRNA class. These esRNAs are produced by a degradation pathway in which the RdRP proteins signal specific transcripts that will be degraded by a newly identified RNase. This RNase, named R3B2, presents unique domain architecture, can only be found in basal fungi and it is also involved in the canonical dicer-dependent RNAi pathway. Our results expand the role of RdRPs in gene silencing and reveal the involvement of these proteins in a new RNA degradation process that could represent the first step in the evolution of RNAi.
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Affiliation(s)
- Trung Anh Trieu
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Silvia Calo
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | | | - Ana Vila
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Simon Moxon
- The Genome Analysis Centre, University of East Anglia, Norwich, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Victoriano Garre
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Rosa M. Ruiz-Vázquez
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
- * E-mail:
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84
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Devert A, Fabre N, Floris M, Canard B, Robaglia C, Crété P. Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified Arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6. PLoS One 2015; 10:e0120100. [PMID: 25793874 PMCID: PMC4368572 DOI: 10.1371/journal.pone.0120100] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/19/2015] [Indexed: 12/05/2022] Open
Abstract
Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ssRNA) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer-independent and primer-dependent RNA polymerase activities with different efficiencies. We further show that RDR2 and RDR6 can initiate dsRNA synthesis either by elongation of 21- to 24- nucleotides RNAs hybridized to complementary RNA template or by elongation of self-primed RNA template. These findings provide new insights into our understanding of the molecular mechanisms of RNA silencing in plants.
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Affiliation(s)
- Anthony Devert
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Nicolas Fabre
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Maïna Floris
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Bruno Canard
- Aix-Marseille Université, AFMB UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - Christophe Robaglia
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Patrice Crété
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
- * E-mail:
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85
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Guan X, Buchholz G, Nick P. Tubulin marker line of grapevine suspension cells as a tool to follow early stress responses. JOURNAL OF PLANT PHYSIOLOGY 2015; 176:118-128. [PMID: 25590686 DOI: 10.1016/j.jplph.2014.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 06/04/2023]
Abstract
Plant microtubules (MTs), in addition to their role in cell division and cell expansion, respond to various stress signals. To understand the biological function of this early response requires non-destructive strategies for visualization in cellular models that are highly responsive to stress signals. We have therefore generated a transgenic tubulin marker line for a cell line from the grapevine Vitis rupestris that readily responds to stress factors of defense-related and abiotic stresses based on a fusion of the green fluorescent protein with Arabidopsis β-tubulin 6. By a combination of spinning-disk confocal microscopy with quantitative image analysis, we could detect early and specific responses of MTs to defense-related and abiotic stress factors in vivo. We observed that Harpin Z (HrpZ), a bacterial elicitor that can trigger programmed cell death, rapidly eliminated radial MTs, followed by a slower depletion of the cortical array. Jasmonic acid (JA), in contrast, induced bundling of cortical MTs. Auxin reduced the thickness of cortical MTs. This effect followed a characteristic bell-shaped dose-dependency and could revert JA-induced bundling. Impeded cell expansion as a consequence of stress treatment or superoptimal auxin was linked with the appearance of intranuclear tubulin speckles. The early and stimulus-specific responses of MTs are discussed with respect to a function in processing or decoding of stress signals.
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Affiliation(s)
- Xin Guan
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Kaiserstraße 2, D-76128 Karlsruhe, Germany.
| | - Günther Buchholz
- RLP AgroScience/AlPlanta - Institute for Plant Research, Breitenweg 71, D-67435 Neustadt an der Weinstraße, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Kaiserstraße 2, D-76128 Karlsruhe, Germany
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86
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Martínez de Alba AE, Moreno AB, Gabriel M, Mallory AC, Christ A, Bounon R, Balzergue S, Aubourg S, Gautheret D, Crespi MD, Vaucheret H, Maizel A. In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs. Nucleic Acids Res 2015; 43:2902-13. [PMID: 25694514 PMCID: PMC4357720 DOI: 10.1093/nar/gkv119] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 01/16/2015] [Accepted: 02/04/2015] [Indexed: 01/24/2023] Open
Abstract
Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5' cap structure and their subsequent 5' to 3' degradation in cytoplasmic processing (P-)bodies. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to double-stranded RNAs by the cellular RNA-dependent RNA polymerase 6 (RDR6) in cytoplasmic siRNA-bodies. PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. We show that the lethality of decapping mutants is suppressed by impairing RDR6 activity. We establish that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of rqc-siRNAs, that over-accumulate when RQC processes are impaired, a subset of which depending on RDR6 for their production. We observe that P- and siRNA-bodies often are dynamically juxtaposed, potentially allowing for cross-talk of the two machineries. Our results suggest that the decapping of endogenous RNA limits their entry into the PTGS pathway. We anticipate that the rqc-siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Gene Expression Regulation, Plant
- Mutation
- Oligonucleotide Array Sequence Analysis
- Plants, Genetically Modified
- RNA Caps/genetics
- RNA Caps/metabolism
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Transcriptome
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Affiliation(s)
| | - Ana Beatriz Moreno
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Marc Gabriel
- Institute for Integrative Biology of the Cell, UMR 9198 - Universite Paris-Sud, Gif-sur-Yvette, France
| | - Allison C Mallory
- Institut Jean-Pierre Bourgin UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Aurélie Christ
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Rémi Bounon
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Sebastien Aubourg
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, UMR 9198 - Universite Paris-Sud, Gif-sur-Yvette, France
| | - Martin D Crespi
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Alexis Maizel
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France Center for Organismal Studies, University of Heidelberg, Germany
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87
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Dey KK, Borth WB, Melzer MJ, Wang ML, Hu JS. Analysis of pineapple mealybug wilt associated virus -1 and -2 for potential RNA silencing suppressors and pathogenicity factors. Viruses 2015; 7:969-95. [PMID: 25751306 PMCID: PMC4379557 DOI: 10.3390/v7030969] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/05/2015] [Accepted: 02/15/2015] [Indexed: 01/02/2023] Open
Abstract
Higher plants use RNA silencing to defend against viral infections. As a counter defense, plant viruses have evolved proteins that suppress RNA silencing. Mealybug wilt of pineapple (MWP), an important disease of pineapple, has been associated with at least three distinct viruses, Pineapple mealybug wilt associated virus -1, -2, and -3 (PMWaV-1, -2, and -3). Selected open reading frames (ORFs) of PMWaV-1 and PMWaV-2 were screened for their local and systemic suppressor activities in Agrobacterium-mediated transient assays using green fluorescent protein (GFP) in Nicotiana benthamiana. Results indicate that PMWaV-2 utilizes a multiple-component RNA silencing suppression mechanism. Two proteins, p20 and CP, target both local and systemic silencing in N. benthamiana, while the p22 and CPd proteins target only systemic silencing. In the related virus PMWaV-1, we found that only one of the encoded proteins, p61, had only systemic suppressor activity. Of all the proteins tested from both viruses, only the PMWaV-2 p20 protein suppressed local silencing induced by double-stranded RNA (dsRNA), but only when low levels of inducing dsRNA were used. None of the proteins analyzed could interfere with the short distance spread of silencing. We examined the mechanism of systemic suppression activity by investigating the effect of PMWaV-2-encoded p20 and CP proteins on secondary siRNAs. Our results suggest that the PMWaV-2 p20 and CP proteins block the systemic silencing signal by repressing production of secondary siRNAs. We also demonstrate that the PMWaV-2 p20 and p22 proteins enhanced the pathogenicity of Potato virus X in N. benthamiana.
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Affiliation(s)
- Kishore K Dey
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Wayne B Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Ming-Li Wang
- Hawaii Agricultural Research Center, Kunia, Honolulu, HI 96797, USA.
| | - John S Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
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88
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Kumar S, AlAbed D, Whitteck JT, Chen W, Bennett S, Asberry A, Wang X, DeSloover D, Rangasamy M, Wright TR, Gupta M. A combinatorial bidirectional and bicistronic approach for coordinated multi-gene expression in corn. PLANT MOLECULAR BIOLOGY 2015; 87:341-53. [PMID: 25657118 DOI: 10.1007/s11103-015-0281-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 12/31/2014] [Indexed: 05/22/2023]
Abstract
Transgene stacking in trait development process through genetic engineering is becoming complex with increased number of desired traits and multiple modes of action for each trait. We demonstrate here a novel gene stacking strategy by combining bidirectional promoter (BDP) and bicistronic approaches to drive coordinated expression of multi-genes in corn. A unidirectional promoter, Ubiquitin-1 (ZMUbi1), from Zea mays was first converted into a synthetic BDP, such that a single promoter can direct the expression of two genes from each end of the promoter. The BDP system was then combined with a bicistronic organization of genes at both ends of the promoter by using a Thosea asigna virus 2A auto-cleaving domain. With this gene stacking configuration, we have successfully obtained expression in transgenic corn of four transgenes; three transgenes conferring insect (cry34Ab1 and cry35Ab1) and herbicide (aad1) resistance, and a phiyfp reporter gene using a single ZMUbi1 bidirectional promoter. Gene expression analyses of transgenic corn plants confirmed better coordinated expression of the four genes compared to constructs driving each gene by independent unidirectional ZmUbi1 promoter. To our knowledge, this is the first report that demonstrates application of a single promoter for co-regulation of multiple genes in a crop plant. This stacking technology would be useful for engineering metabolic pathways both for basic and applied research.
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Affiliation(s)
- Sandeep Kumar
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA,
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89
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Dalakouras A, Dadami E, Wassenegger M. Engineering viroid resistance. Viruses 2015; 7:634-46. [PMID: 25674769 PMCID: PMC4353907 DOI: 10.3390/v7020634] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 01/30/2015] [Indexed: 12/31/2022] Open
Abstract
Viroids are non-encapsidated, non-coding, circular, single-stranded RNAs (ssRNAs). They are classified into the families Pospiviroidae and Avsunviroidae, whose members replicate in the nucleus and chloroplast of plant cells, respectively. Viroids have a wide host range, including crop and ornamental plants, and can cause devastating diseases with significant economic losses. Thus, several viroids are world-wide, classified as quarantine pathogens and, hence, there is an urgent need for the development of robust antiviroid strategies. RNA silencing-based technologies seem to be a promising tool in this direction. Here, we review the recent advances concerning the complex interaction of viroids with the host's RNA silencing machinery, evaluate past and present antiviroid approaches, and finally suggest alternative strategies that could potentially be employed in the future in order to achieve transgenic and non-transgenic viroid-free plants.
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Affiliation(s)
- Athanasios Dalakouras
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, 67435, Germany.
| | - Elena Dadami
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, 67435, Germany.
| | - Michael Wassenegger
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, Germany and Centre for Organisational Studies (COS) Heidelberg, University of Heidelberg, Heidelberg, 69120, Germany.
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90
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Zhao H, Li QQ. In vitro analysis of cleavage and polyadenylation in Arabidopsis. Methods Mol Biol 2015; 1255:79-89. [PMID: 25487206 DOI: 10.1007/978-1-4939-2175-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In eukaryotes, pre-messenger RNA (pre-mRNA) cleavage and polyadenylation is one of the necessary processing steps that produce a mature and functional mRNA. Regulation on pre-mRNA cleavage and polyadenylation affects other processes such as mRNA translocation, stability, and translation. The process of pre-mRNA cleavage and polyadenylation, and its relationship with RNA splicing and translation, have been extensively studied due to its importance in vivo. A successful in vitro system has provided enormous amount of information to the study of cleavage and polyadenylation in the mammalian and yeast systems. Here, we describe an in vitro pre-mRNA cleavage system that faithfully cleaves pre-mRNA substrate using Arabidopsis cell/tissue cultures.
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Affiliation(s)
- Hongwei Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China,
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91
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Ruiz-Vázquez RM, Nicolás FE, Torres-Martínez S, Garre V. Distinct RNAi Pathways in the Regulation of Physiology and Development in the Fungus Mucor circinelloides. ADVANCES IN GENETICS 2015; 91:55-102. [DOI: 10.1016/bs.adgen.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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92
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Boesler B, Meier D, Förstner KU, Friedrich M, Hammann C, Sharma CM, Nellen W. Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. J Biol Chem 2014; 289:35124-38. [PMID: 25352599 DOI: 10.1074/jbc.m114.612663] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA- strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA- strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA-/agnB- double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA- strains was observed.
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Affiliation(s)
- Benjamin Boesler
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Doreen Meier
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Konrad U Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Michael Friedrich
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Laboratory, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University, Campus Ring 1, DE-28759 Bremen, Germany
| | - Cynthia M Sharma
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Wolfgang Nellen
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany,
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93
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Abstract
The ability to distinguish self from non-self nucleic acids enables eukaryotes to suppress mobile elements and maintain genome integrity. In organisms from protist to human, this function is performed by RNA silencing pathways. There have been major advances in our understanding of the RNA silencing machinery, but the mechanisms by which these pathways distinguish self from non-self remain unclear. Recent studies in the yeast C. neoformans indicate that transposon-derived transcripts encode suboptimal introns and tend to stall in spliceosomes, which promotes the biogenesis of siRNA that targets these transcripts. These findings identify gene expression signal strength as a metric by which a foreign element can be distinguished from a host gene, and reveal a new function for introns and the spliceosome in genome defense. Anticipating that these principles may apply to RNA silencing in other systems, we discuss strong hints in the literature suggesting that the spliceosome may guide small RNA biogenesis in the siRNA and piRNA pathways of plants and animals.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
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94
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Sohn SH, Frost J, Kim YH, Choi SK, Lee Y, Seo MS, Lim SH, Choi Y, Kim KH, Lomonossoff G. Cell-autonomous-like silencing of GFP-partitioned transgenic Nicotiana benthamiana. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4271-83. [PMID: 24868037 DOI: 10.1093/jxb/eru200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We previously reported the novel partitioning of regional GFP-silencing on leaves of 35S-GFP transgenic plants, coining the term "partitioned silencing". We set out to delineate the mechanism of partitioned silencing. Here, we report that the partitioned plants were hemizygous for the transgene, possessing two direct-repeat copies of 35S-GFP. The detection of both siRNA expression (21 and 24 nt) and DNA methylation enrichment specifically at silenced regions indicated that both post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) were involved in the silencing mechanism. Using in vivo agroinfiltration of 35S-GFP/GUS and inoculation of TMV-GFP RNA, we demonstrate that PTGS, not TGS, plays a dominant role in the partitioned silencing, concluding that the underlying mechanism of partitioned silencing is analogous to RNA-directed DNA methylation (RdDM). The initial pattern of partitioned silencing was tightly maintained in a cell-autonomous manner, although partitioned-silenced regions possess a potential for systemic spread. Surprisingly, transcriptome profiling through next-generation sequencing demonstrated that expression levels of most genes involved in the silencing pathway were similar in both GFP-expressing and silenced regions although a diverse set of region-specific transcripts were detected.This suggests that partitioned silencing can be triggered and regulated by genes other than the genes involved in the silencing pathway.
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Affiliation(s)
- Seong-Han Sohn
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Jennifer Frost
- College of Natural Resources, University of California, Berkeley CA94720, USA
| | - Yoon-Hee Kim
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Seung-Kook Choi
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Yi Lee
- College of Agricultural, Life and Environmental Sciences, Chungbuk National University, Cheongju 361-763, Korea
| | - Mi-Suk Seo
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Sun-Hyung Lim
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Kook-Hyung Kim
- College of Agriculture and Life Sciences (CALS), Seoul National University, Seoul 151-747, Korea
| | - George Lomonossoff
- Department of Biological Chemistry, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
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95
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Dadami E, Dalakouras A, Zwiebel M, Krczal G, Wassenegger M. An endogene-resembling transgene is resistant to DNA methylation and systemic silencing. RNA Biol 2014; 11:934-41. [PMID: 25180820 PMCID: PMC4179966 DOI: 10.4161/rna.29623] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/11/2014] [Accepted: 06/17/2014] [Indexed: 11/19/2022] Open
Abstract
In plants, endogenes are less prone to RNA silencing than transgenes. While both can be efficiently targeted by small RNAs for post-transcriptional gene silencing (PTGS), generally only transgene PTGS is accompanied by transitivity, RNA-directed DNA methylation (RdDM) and systemic silencing. In order to investigate whether a transgene could mimick an endogene and thus be less susceptible to RNA silencing, we generated an intron-containing, endogene-resembling GREEN FLUORESCENT PROTEIN (GFP) transgene (GFP(endo)). Upon agroinfiltration of a hairpin GFP (hpF) construct, transgenic Nicotiana benthamiana plants harboring GFP(endo) (Nb-GFP(endo)) were susceptible to local PTGS. Yet, in the local area, PTGS was not accompanied by RdDM of the GFP(endo) coding region. Importantly, hpF-agroinfiltrated Nb-GFP(endo) plants were resistant to systemic silencing. For reasons of comparison, transgenic N. benthamiana plants (Nb-GFP(cDNA)) carrying a GFP cDNA transgene (GFP(cDNA)) were included in the analysis. HpF-agroinfiltrated Nb-GFP(cDNA) plants exhibited local PTGS and RdDM. In addition, systemic silencing was established in Nb-GFP(cDNA) plants. In agreement with previous reports using grafted scions, in systemically silenced tissue, siRNAs mapping to the 3' of GFP were predominantly detectable by Northern blot analysis. Yet, in contrast to other reports, in systemically silenced leaves, PTGS was also accompanied by dense RdDM comprising the entire GFP(cDNA) coding region. Overall, our analysis indicated that cDNA transgenes are prone to systemic PTGS and RdDM, while endogene-resembling ones are resistant to RNA silencing.
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Affiliation(s)
- Elena Dadami
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | | | - Michele Zwiebel
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | - Gabi Krczal
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
| | - Michael Wassenegger
- RLP AgroScience GmbH; AlPlanta-Institute for Plant Research; Neustadt, Germany
- Centre for Organismal Studies (COS) Heidelberg; University of Heidelberg; Heidelberg, Germany
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96
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Connecting the dots of RNA-directed DNA methylation in Arabidopsis thaliana. Chromosome Res 2014; 22:225-40. [PMID: 24846724 DOI: 10.1007/s10577-014-9425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Noncoding RNAs are the rising stars of genome regulation and are crucial to an organism's metabolism, development, and defense. One of their most notable functions is its ability to direct epigenetic modifications through small RNA molecules to specific genomic regions, ensuring transcriptional regulation, proper genome organization, and maintenance of genome integrity. Here, we review the current knowledge of the spatial organization of the Arabidopsis thaliana RNA-directed DNA methylation pathway within the cell nucleus, which, while known to be essential for the proper establishment of epigenetic modifications, remains poorly understood. We will also discuss possible future cytological approaches that have the potential of unveiling functional insights into how small RNA-directed epigenetics is regulated through the spatiotemporal regulation of its major components within the cell.
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97
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Dugdale B, Mortimer CL, Kato M, James TA, Harding RM, Dale JL. Design and construction of an in-plant activation cassette for transgene expression and recombinant protein production in plants. Nat Protoc 2014; 9:1010-27. [PMID: 24705598 DOI: 10.1038/nprot.2014.068] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virus-based transgene expression systems have become particularly valuable for recombinant protein production in plants. The dual-module in-plant activation (INPACT) expression platform consists of a uniquely designed split-gene cassette incorporating the cis replication elements of Tobacco yellow dwarf geminivirus (TYDV) and an ethanol-inducible activation cassette encoding the TYDV Rep and RepA replication-associated proteins. The INPACT system is essentially tailored for recombinant protein production in stably transformed plants and provides both inducible and high-level transient transgene expression with the potential to be adapted to diverse crop species. The construction of a novel split-gene cassette, the inducible nature of the system and the ability to amplify transgene expression via rolling-circle replication differentiates this system from other DNA- and RNA-based virus vector systems used for stable or transient recombinant protein production in plants. Here we provide a detailed protocol describing the design and construction of a split-gene INPACT cassette, and we highlight factors that may influence optimal activation and amplification of gene expression in transgenic plants. By using Nicotiana tabacum, the protocol takes 6-9 months to complete, and recombinant proteins expressed using INPACT can accumulate to up to 10% of the leaf total soluble protein.
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Affiliation(s)
- Benjamin Dugdale
- 1] Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia. [2]
| | - Cara L Mortimer
- 1] Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia. [2]
| | - Maiko Kato
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tess A James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Robert M Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - James L Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
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98
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Shao F, Lu S. Identification, molecular cloning and expression analysis of five RNA-dependent RNA polymerase genes in Salvia miltiorrhiza. PLoS One 2014; 9:e95117. [PMID: 24733018 PMCID: PMC3986363 DOI: 10.1371/journal.pone.0095117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/27/2014] [Indexed: 12/31/2022] Open
Abstract
RNA-dependent RNA polymerases (RDRs) act as key components of the small RNA biogenesis pathways and play significant roles in post-transcriptional gene silencing (PTGS) and antiviral defense. However, there is no information about the RDR gene family in Salvia miltiorrhiza, an emerging model medicinal plant with great economic value. Through genome-wide predication and subsequent molecular cloning, five full-length S. miltiorrhiza RDR genes, termed SmRDR1–SmRDR5, were identified. The length of SmRDR cDNAs varies between 3,262 (SmRDR5) and 4,130 bp (SmRDR3). The intron number of SmRDR genes varies from 3 (SmRDR1, SmRDR3 and SmRDR4) to 17 (SmRDR5). All of the deduced SmRDR protein sequences contain the conserved RdRp domain. Moreover, SmRDR2 and SmRDR4 have an additional RRM domain. Based on the phylogenetic tree constructed with sixteen RDRs from Arabidopsis, rice and S. miltiorrhiza, plant RDRs may be divided into four groups (RDR1–RDR4). The RDR1 group contains an AtRDR and an OsRDR, while includes two SmRDRs. On the contrary, the RDR3 group contains three AtRDRs and two OsRDRs, but has only one SmRDR. SmRDRs were differentially expressed in flowers, leaves, stems and roots of S. miltiorrhiza and responsive to methyl jasmonate treatment and cucumber mosaic virus infection. The results suggest the involvement of RDRs in S. miltiorrhiza development and response to abiotic and biotic stresses. It provides a foundation for further studying the regulation and biological functions of SmRDRs and the biogenesis pathways of small RNAs in S. miltiorrhiza.
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Affiliation(s)
- Fenjuan Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail:
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99
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Mendoza-Poudereux I, Muñoz-Bertomeu J, Navarro A, Arrillaga I, Segura J. Enhanced levels of S-linalool by metabolic engineering of the terpenoid pathway in spike lavender leaves. Metab Eng 2014; 23:136-44. [PMID: 24685653 DOI: 10.1016/j.ymben.2014.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/03/2014] [Accepted: 03/20/2014] [Indexed: 11/17/2022]
Abstract
Transgenic Lavandula latifolia plants overexpressing the linalool synthase (LIS) gene from Clarkia breweri, encoding the LIS enzyme that catalyzes the synthesis of linalool were generated. Most of these plants increased significantly their linalool content as compared to controls, especially in the youngest leaves, where a linalool increase up to a 1000% was observed. The phenotype of increased linalool content observed in young leaves was maintained in those T1 progenies that inherit the LIS transgene, although this phenotype was less evident in the flower essential oil. Cross-pollination of transgenic spike lavender plants allowed the generation of double transgenic plants containing the DXS (1-deoxy-d-xylulose-5-P synthase), coding for the first enzyme of the methyl-d-erythritol-4-phosphate pathway, and LIS genes. Both essential oil yield and linalool content in double DXS-LIS transgenic plants were lower than that of their parentals, which could be due to co-suppression effects linked to the structures of the constructs used.
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Affiliation(s)
- Isabel Mendoza-Poudereux
- Departamento de Biología Vegetal, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain; ISIC/ERI de Biotecnología y Biomedicina, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain
| | - Jesús Muñoz-Bertomeu
- Instituto de Biología Molecular y Celular de Plantas, Departamento Biotecnología, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, C/Ingeniero Fausto Elio, 46022 Valencia, Spain
| | - Alicia Navarro
- Departamento de Biología Vegetal, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain; ISIC/ERI de Biotecnología y Biomedicina, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain
| | - Isabel Arrillaga
- Departamento de Biología Vegetal, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain; ISIC/ERI de Biotecnología y Biomedicina, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain
| | - Juan Segura
- Departamento de Biología Vegetal, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain; ISIC/ERI de Biotecnología y Biomedicina, Universidad de Valencia, Av. Vicent Andrés Estellés S/N, Burjasot, 46100 Valencia, Spain.
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100
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Li F, Huang C, Li Z, Zhou X. Suppression of RNA silencing by a plant DNA virus satellite requires a host calmodulin-like protein to repress RDR6 expression. PLoS Pathog 2014; 10:e1003921. [PMID: 24516387 PMCID: PMC3916407 DOI: 10.1371/journal.ppat.1003921] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/24/2013] [Indexed: 11/19/2022] Open
Abstract
In plants, RNA silencing plays a key role in antiviral defense. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that target different effector molecules in the RNA silencing pathway. Evidence has shown that plants also encode endogenous suppressors of RNA silencing (ESRs) that function in proper regulation of RNA silencing. The possibility that these cellular proteins can be subverted by viruses to thwart host defense is intriguing but has not been fully explored. Here we report that the Nicotiana benthamiana calmodulin-like protein Nbrgs-CaM is required for the functions of the VSR βC1, the sole protein encoded by the DNA satellite associated with the geminivirus Tomato yellow leaf curl China virus (TYLCCNV). Nbrgs-CaM expression is up-regulated by the βC1. Transgenic plants over-expressing Nbrgs-CaM displayed developmental abnormities reminiscent of βC1-associated morphological alterations. Nbrgs-CaM suppressed RNA silencing in an Agrobacterium infiltration assay and, when over-expressed, blocked TYLCCNV-induced gene silencing. Genetic evidence showed that Nbrgs-CaM mediated the βC1 functions in silencing suppression and symptom modulation, and was required for efficient virus infection. Moreover, the tobacco and tomato orthologs of Nbrgs-CaM also possessed ESR activity, and were induced by betasatellite to promote virus infection in these Solanaceae hosts. We further demonstrated that βC1-induced Nbrgs-CaM suppressed the production of secondary siRNAs, likely through repressing RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) expression. RDR6-deficient N. benthamiana plants were defective in antiviral response and were hypersensitive to TYLCCNV infection. More significantly, TYLCCNV could overcome host range restrictions to infect Arabidopsis thaliana when the plants carried a RDR6 mutation. These findings demonstrate a distinct mechanism of VSR for suppressing PTGS through usurpation of a host ESR, and highlight an essential role for RDR6 in RNA silencing defense response against geminivirus infection.
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Affiliation(s)
- Fangfang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Changjun Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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