1
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Li XM, Jenke H, Strauss S, Wang Y, Bhatia N, Kierzkowski D, Lymbouridou R, Huijser P, Smith RS, Runions A, Tsiantis M. Age-associated growth control modifies leaf proximodistal symmetry and enabled leaf shape diversification. Curr Biol 2024:S0960-9822(24)01007-8. [PMID: 39216485 DOI: 10.1016/j.cub.2024.07.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/21/2024] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Biological shape diversity is often manifested in modulation of organ symmetry and modification of the patterned elaboration of repeated shape elements.1,2,3,4,5 Whether and how these two aspects of shape determination are coordinately regulated is unclear.5,6,7 Plant leaves provide an attractive system to investigate this problem, because they often show asymmetries along the proximodistal (PD) axis of their blades, along which they can also produce repeated marginal outgrowths such as serrations or leaflets.1 One aspect of leaf shape diversity is heteroblasty, where the leaf form in a single genotype is modified with progressive plant age.8,9,10,11 In Arabidopsis thaliana, a plant with simple leaves, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9) controls heteroblasty by activating CyclinD3 expression, thereby sustaining proliferative growth and retarding differentiation in adult leaves.12,13 However, the precise significance of SPL9 action for leaf symmetry and marginal patterning is unknown. By combining genetics, quantitative shape analyses, and time-lapse imaging, we show that PD symmetry of the leaf blade in A. thaliana decreases in response to an age-dependent SPL9 expression gradient, and that SPL9 action coordinately regulates the distribution and shape of marginal serrations and overall leaf form. Using comparative analyses, we demonstrate that heteroblastic growth reprogramming in Cardamine hirsuta, a complex-leafed relative of A. thaliana, also involves prolonging the duration of cell proliferation and delaying differentiation. We further provide evidence that SPL9 enables species-specific action of homeobox genes that promote leaf complexity. In conclusion, we identified an age-dependent layer of organ PD growth regulation that modulates leaf symmetry and has enabled leaf shape diversification.
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Affiliation(s)
- Xin-Min Li
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Hannah Jenke
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Yi Wang
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Neha Bhatia
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Rena Lymbouridou
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Adam Runions
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany.
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2
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Johnson A, Mcassey E, Diaz S, Reagin J, Redd PS, Parrilla DR, Nguyen H, Stec A, McDaniel LAL, Clemente TE, Stupar RM, Parrott WA, Hancock CN. Development of mPing-based activation tags for crop insertional mutagenesis. PLANT DIRECT 2021; 5:e00300. [PMID: 33506165 PMCID: PMC7814626 DOI: 10.1002/pld3.300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system.
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Affiliation(s)
- Alexander Johnson
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Edward Mcassey
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
- Present address:
School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHIUSA
| | - Stephanie Diaz
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
- Present address:
Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Jacob Reagin
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
| | - Priscilla S. Redd
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
| | - Daymond R. Parrilla
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
- Present address:
Department of Molecular and Comparative PathobiologyJohns Hopkins School of MedicineBaltimoreMDUSA
| | - Hanh Nguyen
- Department of Agronomy and Horticulture/Center for Plant Science InnovationUniversity of NebraskaLincolnNEUSA
| | - Adrian Stec
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Lauren A. L. McDaniel
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture/Center for Plant Science InnovationUniversity of NebraskaLincolnNEUSA
| | - Robert M. Stupar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Wayne A. Parrott
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - C. Nathan Hancock
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
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3
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Borrill P. Blurring the boundaries between cereal crops and model plants. THE NEW PHYTOLOGIST 2020; 228:1721-1727. [PMID: 31571228 DOI: 10.1111/nph.16229] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
The cereal crops rice (Oryza sativa), maize (Zea mays ssp. mays) and wheat (Triticum aestivum) provide half of the food eaten by humankind. However, understanding their biology has proved challenging due to their large size, long lifecycle and large genomes. The model plant Arabidopsis thaliana avoids these practical problems and has provided fundamental understanding of plant biology, however not all of this knowledge is directly transferrable to cereals. Recent developments in gene editing, speed breeding and genome assembly techniques mean that the challenges associated with working with the major cereal crops can be overcome. Resources such as mutant collections and genome sequences are now available for these crops, making them attractive experimental systems with which to make discoveries that are directly applicable to increasing crop production.
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Affiliation(s)
- Philippa Borrill
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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4
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Sahu PK, Sao R, Mondal S, Vishwakarma G, Gupta SK, Kumar V, Singh S, Sharma D, Das BK. Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review. PLANTS 2020; 9:plants9101355. [PMID: 33066352 PMCID: PMC7602136 DOI: 10.3390/plants9101355] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022]
Abstract
The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sudhir Kumar Gupta
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India;
| | - Sudhir Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
- Correspondence: (D.S.); (B.K.D.)
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
- Correspondence: (D.S.); (B.K.D.)
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5
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Nilsson AK, Andersson MX. The pht4;1-3 mutant line contains a loss of function allele in the Fatty Acid Desaturase 7 gene caused by a remnant inactivated selection marker-a cautionary tale. PeerJ 2017; 5:e4134. [PMID: 29209580 PMCID: PMC5713625 DOI: 10.7717/peerj.4134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/13/2017] [Indexed: 11/20/2022] Open
Abstract
A striking and unexpected biochemical phenotype was found in an insertion mutant line in the model plant Arabidopsis thaliana. One of two investigated insertion mutant lines in the gene encoding the phosphate transporter PHT4;1 demonstrated a prominent loss of trienoic fatty acids, whereas the other insertion line was indistinguishable from wild type in this aspect. We demonstrate that the loss of trienoic fatty acids was due to a remnant inactive negative selection marker gene in this particular transposon tagged line, pht4;1-3. This constitutes a cautionary tale that warns of the importance to confirm the loss of this type of selection markers and the importance of verifying the relationship between a phenotype and genotype by more than one independent mutant line or alternatively genetic complementation.
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Affiliation(s)
- Anders K Nilsson
- Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Mats X Andersson
- Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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6
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Tavakol E. Virus-Induced Gene Silencing (VIGS) in Aegilops tauschii and Its Use in Functional Analysis of AetDREB2. Mol Biotechnol 2017; 60:41-48. [PMID: 29196985 DOI: 10.1007/s12033-017-0042-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Among the available reverse genetic approaches for studying gene function, virus-induced gene silencing (VIGS) has several advantages. It allows rapid characterization of gene function independent of stable transformation, which is basically difficult to achieve in monocots, and offers the potential to silence individual or multiple genes of a gene family. In order to establish a VIGS system in Aegilops tauschii, modified vectors derived from Barley stripe mosaic virus (BSMV) were used for silencing a phytoene desaturase gene that provides a convenient visual reporter for silencing. The results demonstrated a high efficiency of BSMV-VIGS in A. tauschii. Moreover, the BSMV-VIGS system was used to target a 354 bp specific region of the Dehydration-responsive element-binding (AetDreb2) gene, resulting in successful silencing of the gene in A. tauschii plants, as verified by real-time qRT-PCR. Indeed, in comparison with plants that were inoculated with an empty vector (BSMV:00), a faster rate of wilting and a lower relative water content were observed in plants inoculated with BSMV:AetDreb2 when they were exposed to drought stress. Therefore, BSMV-VIGS can be efficiently employed as a novel tool for reverse genetics in A. tauschii. It can also be used to study the effects of polyploidization on the gene function by a comparative analysis between bread wheat and its diploid progenitor.
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Affiliation(s)
- Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186, Shiraz, Iran.
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7
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Pérez‐Martín F, Yuste‐Lisbona FJ, Pineda B, Angarita‐Díaz MP, García‐Sogo B, Antón T, Sánchez S, Giménez E, Atarés A, Fernández‐Lozano A, Ortíz‐Atienza A, García‐Alcázar M, Castañeda L, Fonseca R, Capel C, Goergen G, Sánchez J, Quispe JL, Capel J, Angosto T, Moreno V, Lozano R. A collection of enhancer trap insertional mutants for functional genomics in tomato. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1439-1452. [PMID: 28317264 PMCID: PMC5633825 DOI: 10.1111/pbi.12728] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/03/2017] [Accepted: 03/15/2017] [Indexed: 05/06/2023]
Abstract
With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild type and its mutant; hence, mutant collections are a valuable resource. In this sense, T-DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T-DNA collection in tomato (Solanum lycopersicum L.), which has been produced by Agrobacterium-mediated transformation using a binary vector bearing a minimal promoter fused to the uidA reporter gene. Two genes have been isolated from different T-DNA mutants, one of these genes codes for a UTP-glucose-1-phosphate uridylyltransferase involved in programmed cell death and leaf development, which means a novel gene function reported in tomato. Together, our results support that enhancer trapping is a powerful tool to identify novel genes and regulatory elements in tomato and that this T-DNA mutant collection represents a highly valuable resource for functional analyses in this fleshy-fruited model species.
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Affiliation(s)
- Fernando Pérez‐Martín
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | | | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - María Pilar Angarita‐Díaz
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Begoña García‐Sogo
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Teresa Antón
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Sibilla Sánchez
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Estela Giménez
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Alejandro Atarés
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Antonia Fernández‐Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Ana Ortíz‐Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Manuel García‐Alcázar
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Laura Castañeda
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Rocío Fonseca
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Geraldine Goergen
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Jorge Sánchez
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Jorge L. Quispe
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
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8
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Mapping of T-DNA and Ac/Ds by TAIL-PCR to Analyze Chromosomal Rearrangements. Methods Mol Biol 2016. [PMID: 27557698 DOI: 10.1007/978-1-4939-4931-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Insertion mutagenesis using known DNA sequences such as T-DNA and transposons is an important tool for studies on gene function in plant sciences. The transposons Activator (Ac)/Dissociation (Ds) have been systematically used to manipulate plant chromosomes. For both of these applications, the recovery of genomic DNA sequences flanking the insertions is required to estimate the sizes and/or scales of the reconstituted chromosomes. In this chapter, we describe the protocols for thermal asymmetric interlaced PCR (TAIL-PCR) for isolation of genomic sequences flanking DNA inserts in plant genomes.
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9
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Murphy E, Vu LD, Van den Broeck L, Lin Z, Ramakrishna P, van de Cotte B, Gaudinier A, Goh T, Slane D, Beeckman T, Inzé D, Brady SM, Fukaki H, De Smet I. RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4863-75. [PMID: 27521602 PMCID: PMC4983113 DOI: 10.1093/jxb/erw281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In plants, many signalling molecules, such as phytohormones, miRNAs, transcription factors, and small signalling peptides, drive growth and development. However, very few small signalling peptides have been shown to be necessary for lateral root development. Here, we describe the role of the peptide RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle. Our results further suggest that this small signalling peptide acts on the transcriptional cascade leading to a new lateral root upstream of GATA23, an important player in lateral root formation. In addition, we describe a role for ETHYLENE RESPONSE FACTORs (ERFs) in regulating RALFL34 expression. Taken together, we put forward RALFL34 as a new, important player in lateral root initiation.
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Affiliation(s)
- Evan Murphy
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Lam Dai Vu
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Lisa Van den Broeck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Zhefeng Lin
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Brigitte van de Cotte
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tatsuaki Goh
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, D- 72076 Tübingen, Germany
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK
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10
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Choi K, Reinhard C, Serra H, Ziolkowski PA, Underwood CJ, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP, Henderson IR. Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet 2016; 12:e1006179. [PMID: 27415776 PMCID: PMC4945094 DOI: 10.1371/journal.pgen.1006179] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/15/2016] [Indexed: 12/31/2022] Open
Abstract
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Carsten Reinhard
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Charles J. Underwood
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Xiaohui Zhao
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Thomas J. Hardcastle
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Griffin
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Jackson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles, France
| | - Gil McVean
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ian R. Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
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11
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Ondzighi-Assoume CA, Chakraborty S, Harris JM. Environmental Nitrate Stimulates Abscisic Acid Accumulation in Arabidopsis Root Tips by Releasing It from Inactive Stores. THE PLANT CELL 2016; 28:729-45. [PMID: 26887919 PMCID: PMC4826012 DOI: 10.1105/tpc.15.00946] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/01/2016] [Accepted: 02/16/2016] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) signaling plays a major role in root system development, regulating growth and root architecture. However, the precise localization of ABA remains undetermined. Here, we present a mechanism in which nitrate signaling stimulates the release of bioactive ABA from the inactive storage form, ABA-glucose ester (ABA-GE). We found that ABA accumulated in the endodermis and quiescent center of Arabidopsis thaliana root tips, mimicking the pattern of SCARECROW expression, and (to lower levels) in the vascular cylinder. Nitrate treatment increased ABA levels in root tips; this stimulation requires the activity of the endoplasmic reticulum-localized, ABA-GE-deconjugating enzyme b-GLUCOSIDASE1, but not de novo ABA biosynthesis. Immunogold labeling demonstrated that ABA is associated with cytoplasmic structures near, but not within, the endoplasmic reticulum. These findings demonstrate a mechanism for nitrate-regulated root growth via regulation of ABA accumulation in the root tip, providing insight into the environmental regulation of root growth.
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Affiliation(s)
- Christine A Ondzighi-Assoume
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405 Department of Plant Sciences, The University of Tennessee, Knoxville, Tennessee 37996
| | - Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405
| | - Jeanne M Harris
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405
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12
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Randall RS, Miyashima S, Blomster T, Zhang J, Elo A, Karlberg A, Immanen J, Nieminen K, Lee JY, Kakimoto T, Blajecka K, Melnyk CW, Alcasabas A, Forzani C, Matsumoto-Kitano M, Mähönen AP, Bhalerao R, Dewitte W, Helariutta Y, Murray JAH. AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins. Biol Open 2015; 4:1229-36. [PMID: 26340943 PMCID: PMC4610221 DOI: 10.1242/bio.013128] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.
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Affiliation(s)
- Ricardo S Randall
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Shunsuke Miyashima
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Tiina Blomster
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Jing Zhang
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Annakaisa Elo
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Anna Karlberg
- Department of Plant Physiology, Umeå University, Umeå SE-901 87, Sweden
| | - Juha Immanen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Tatsuo Kakimoto
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Karolina Blajecka
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Charles W Melnyk
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Annette Alcasabas
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Celine Forzani
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Miho Matsumoto-Kitano
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ari Pekka Mähönen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | | | - Walter Dewitte
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Ykä Helariutta
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - James A H Murray
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
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13
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Romani I, Manavski N, Morosetti A, Tadini L, Maier S, Kühn K, Ruwe H, Schmitz-Linneweber C, Wanner G, Leister D, Kleine T. A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU). PLANT PHYSIOLOGY 2015; 169:627-46. [PMID: 26152711 PMCID: PMC4577433 DOI: 10.1104/pp.15.00964] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
Plastid gene expression is crucial for organelle function, but the factors that control it are still largely unclear. Members of the so-called mitochondrial transcription termination factor (mTERF) family are found in metazoans and plants and regulate organellar gene expression at different levels. Arabidopsis (Arabidopsis thaliana) mTERF6 is localized in chloroplasts and mitochondria, and its knockout perturbs plastid development and results in seedling lethality. In the leaky mterf6-1 mutant, a defect in photosynthesis is associated with reduced levels of photosystem subunits, although corresponding messenger RNA levels are unaffected, whereas translational capacity and maturation of chloroplast ribosomal RNAs (rRNAs) are perturbed in mterf6-1 mutants. Bacterial one-hybrid screening, electrophoretic mobility shift assays, and coimmunoprecipitation experiments reveal a specific interaction between mTERF6 and an RNA sequence in the chloroplast isoleucine transfer RNA gene (trnI.2) located in the rRNA operon. In vitro, recombinant mTERF6 bound to its plastid DNA target site can terminate transcription. At present, it is unclear whether disturbed rRNA maturation is a primary or secondary defect. However, it is clear that mTERF6 is required for the maturation of trnI.2. This points to an additional function of mTERFs.
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MESH Headings
- 5' Untranslated Regions/genetics
- Aminoacylation
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Basic-Leucine Zipper Transcription Factors/genetics
- Basic-Leucine Zipper Transcription Factors/metabolism
- Chloroplasts/metabolism
- DNA, Bacterial/genetics
- Gene Expression Regulation, Plant
- Genetic Loci
- Mitochondria/metabolism
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Molecular Sequence Data
- Mutagenesis, Insertional/genetics
- Mutation
- Phenotype
- Photosynthesis
- Protein Binding
- Protein Transport
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- RNA, Transfer, Ile/metabolism
- Ribosomes/metabolism
- Seedlings/metabolism
- Seeds/ultrastructure
- Transcription Termination, Genetic
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Affiliation(s)
- Isidora Romani
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Nikolay Manavski
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Arianna Morosetti
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Luca Tadini
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Swetlana Maier
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Kristina Kühn
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Hannes Ruwe
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Christian Schmitz-Linneweber
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Gerhard Wanner
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
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14
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Tian M, Lou L, Liu L, Yu F, Zhao Q, Zhang H, Wu Y, Tang S, Xia R, Zhu B, Serino G, Xie Q. The RING finger E3 ligase STRF1 is involved in membrane trafficking and modulates salt-stress response in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:81-92. [PMID: 25704231 DOI: 10.1111/tpj.12797] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/28/2015] [Accepted: 02/03/2015] [Indexed: 05/06/2023]
Abstract
Salt stress is a detrimental factor for plant growth and development. The response to salt stress has been shown to involve components in the intracellular trafficking system, as well as components of the ubiquitin-proteasome system (UPS). In this article, we have identified in Arabidopsis thaliana a little reported ubiquitin ligase involved in salt-stress response, which we named STRF1 (Salt Tolerance RING Finger 1). STRF1 is a member of RING-H2 finger proteins and we demonstrate that it has ubiquitin ligase activity in vitro. We also show that STRF1 localizes mainly at the plasma membrane and at the intracellular endosomes. strf1-1 loss-of-function mutant seedlings exhibit accelerated endocytosis in roots, and have altered expression of several genes involved in the membrane trafficking system. Moreover, protein trafficking inhibitor, brefeldin A (BFA), treatment has increased BFA bodies in strf1-1 mutant. This mutant also showed increased tolerance to salt, ionic and osmotic stresses, reduced accumulation of reactive oxygen species during salt stress, and increased expression of AtRbohD, which encodes a nicotinamide adenine dinucleotide phosphate (NADPH) oxidase involved in H2 O2 production. We conclude that STRF1 is a membrane trafficking-related ubiquitin ligase, which helps the plant to respond to salt stress by monitoring intracellular membrane trafficking and reactive oxygen species (ROS) production.
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Affiliation(s)
- Miaomiao Tian
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
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15
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Wu L, Di DW, Zhang D, Song B, Luo P, Guo GQ. Frequent problems and their resolutions by using thermal asymmetric interlaced PCR (TAIL-PCR) to clone genes in Arabidopsis T-DNA tagged mutants. BIOTECHNOL BIOTEC EQ 2015; 29:260-267. [PMID: 26019639 PMCID: PMC4433792 DOI: 10.1080/13102818.2014.998161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/10/2014] [Indexed: 10/27/2022] Open
Abstract
T-DNA insertional mutagenesis is a powerful tool in Arabidopsis functional genomics research. Previous studies have developed thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) as an efficient strategy in isolation of DNA sequences adjacent to known sequences in T-DNA tagged mutants. However, a number of problems are encountered when attempts are made to clone flanking sequences in T-DNA tagged mutants. Therefore, it is necessary to improve the efficiency of cloning mutagenesis. Here, we present the most frequent problems and provide an improved method to increase TAIL-PCR efficiency. Even then, it is not always possible to successfully obtain flanking sequences; in such cases, we recommend using high-throughput sequencing to determine the mutations.
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Affiliation(s)
- Lei Wu
- Department of MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Dong-Wei Di
- Department of MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Dan Zhang
- Department of MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Bin Song
- Department of MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
- Department of Life Science College, Xiamen University, Xiamen, Fujian, P.R. China
| | - Pan Luo
- Department of MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Guang-Qin Guo
- Department of MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
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16
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Hunter CT, Suzuki M, Saunders J, Wu S, Tasi A, McCarty DR, Koch KE. Phenotype to genotype using forward-genetic Mu-seq for identification and functional classification of maize mutants. FRONTIERS IN PLANT SCIENCE 2014; 4:545. [PMID: 24432026 PMCID: PMC3882665 DOI: 10.3389/fpls.2013.00545] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/12/2013] [Indexed: 05/08/2023]
Abstract
In pursuing our long-term goals of identifying causal genes for mutant phenotypes in maize, we have developed a new, phenotype-to-genotype approach for transposon-based resources, and used this to identify candidate genes that co-segregate with visible kernel mutants. The strategy incorporates a redesigned Mu-seq protocol (sequence-based, transposon mapping) for high-throughput identification of individual plants carrying Mu insertions. Forward-genetic Mu-seq also involves a genetic pipeline for generating families that segregate for mutants of interest, and grid designs for concurrent analysis of genotypes in multiple families. Critically, this approach not only eliminates gene-specific PCR genotyping, but also profiles all Mu-insertions in hundreds of individuals simultaneously. Here, we employ this scalable approach to study 12 families that showed Mendelian segregation of visible seed mutants. These families were analyzed in parallel, and 7 showed clear co-segregation between the selected phenotype and a Mu insertion in a specific gene. Results were confirmed by PCR. Mutant genes that associated with kernel phenotypes include those encoding: a new allele of Whirly1 (a transcription factor with high affinity for organellar and single-stranded DNA), a predicted splicing factor with a KH domain, a small protein with unknown function, a putative mitochondrial transcription-termination factor, and three proteins with pentatricopeptide repeat domains (predicted mitochondrial). Identification of such associations allows mutants to be prioritized for subsequent research based on their functional annotations. Forward-genetic Mu-seq also allows a systematic dissection of mutant classes with similar phenotypes. In the present work, a high proportion of kernel phenotypes were associated with mutations affecting organellar gene transcription and processing, highlighting the importance and non-redundance of genes controlling these aspects of seed development.
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Affiliation(s)
- Charles T. Hunter
- *Correspondence: Charles T. Hunter, Horticultural Sciences, University of Florida, 2550 Hull Rd., Gainesville, FL 32611, USA e-mail:
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17
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Matus JT, Ferrier T, Riechmann JL. Identification of Arabidopsis knockout lines for genes of interest. Methods Mol Biol 2014; 1110:347-362. [PMID: 24395269 DOI: 10.1007/978-1-4614-9408-9_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Determining gene function through reverse genetics has been an important experimental approach in the field of flower development. The method largely relies on the availability of knockout lines for the gene of interest. Insertional mutagenesis can be performed using either T-DNA or transposable elements, but the former has been more frequently employed in Arabidopsis. A primary concern for working with insertional mutant lines is whether the respective insertion results in a complete or rather a partial loss of gene function. The effect of the insertion largely depends on its position with respect to the structure of the gene. In order to quickly identify and obtain knockout lines for genes of interest in Arabidopsis, more than 325,000 mapped insertion lines have been catalogued on indexed libraries and made publicly available to researchers. Online accessible databases provide information regarding the site of insertion, whether a mutant line is available in a homozygous or hemizygous state, and outline technical aspects for plant identification, such as primer design tools used for genotyping. In this chapter, we describe the procedure for isolating knockout lines for genes of interest in Arabidopsis.
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Affiliation(s)
- José Tomás Matus
- Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Universidad Autónoma de Barcelona, Barcelona, Spain
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18
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Takahashi H, Iwakawa H, Ishibashi N, Kojima S, Matsumura Y, Prananingrum P, Iwasaki M, Takahashi A, Ikezaki M, Luo L, Kobayashi T, Machida Y, Machida C. Meta-analyses of microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and their modifying mutants reveal a critical role for the ETT pathway in stabilization of adaxial-abaxial patterning and cell division during leaf development. PLANT & CELL PHYSIOLOGY 2013; 54:418-31. [PMID: 23396601 PMCID: PMC3589830 DOI: 10.1093/pcp/pct027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/01/2013] [Indexed: 05/22/2023]
Abstract
It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial-abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1-AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1-AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1-AS2-ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba, 271-8510 Japan
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
| | - Hidekazu Iwakawa
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
- Present address: Department of Biological Sciences, Purdue University, West, Lafayette, IN 47907-1392, USA
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- These authors contributed equally to this work
| | - Shoko Kojima
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Pratiwi Prananingrum
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Mayumi Iwasaki
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Present address: Department of Plant Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Masaya Ikezaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Takeshi Kobayashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
| | - Chiyoko Machida
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
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Enugutti B, Schneitz K. Genetic analysis of ectopic growth suppression during planar growth of integuments mediated by the Arabidopsis AGC protein kinase UNICORN. BMC PLANT BIOLOGY 2013; 13:2. [PMID: 23281875 PMCID: PMC3560232 DOI: 10.1186/1471-2229-13-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 12/17/2012] [Indexed: 05/22/2023]
Abstract
BACKGROUND The coordination of growth within a tissue layer is of critical importance for tissue morphogenesis. For example, cells within the epidermis undergo stereotypic cell divisions that are oriented along the plane of the layer (planar growth), thereby propagating the layered epidermal structure. Little is known about the developmental control that regulates such planar growth in plants. Recent evidence suggested that the Arabidopsis AGC VIII protein kinase UNICORN (UCN) maintains planar growth by suppressing the formation of ectopic multicellular protrusions in several floral tissues including integuments. In the current model UCN controls this process during integument development by directly interacting with the ABERRANT TESTA SHAPE (ATS) protein, a member of the KANADI (KAN) family of transcription factors, thereby repressing its activity. Here we report on the further characterization of the UCN mechanism. RESULTS Phenotypic analysis of flowers of ucn-1 plants impaired in floral homeotic gene activity revealed that any of the four floral whorls could produce organs carrying ucn-1 protrusions. The ectopic outgrowths of ucn integuments did not accumulate detectable signals of the auxin and cytokinin reporters DR5rev::GFP and ARR5::GUS, respectively. Furthermore, wild-type and ucn-1 seedlings showed similarly strong callus formation upon in vitro culture on callus-inducing medium. We also show that ovules of ucn-1 plants carrying the dominant ats allele sk21-D exhibited more pronounced protrusion formation. Finally ovules of ucn-1 ett-1 double mutants and ucn-1 ett-1 arf4-1 triple mutants displayed an additive phenotype. CONCLUSIONS These data deepen the molecular insight into the UCN-mediated control of planar growth during integument development. The presented evidence indicates that UCN downstream signaling does not involve the control of auxin or cytokinin homeostasis. The results also reveal that UCN interacts with ATS independently of an ATS/ETT complex required for integument initiation and they further emphasize the necessity to balance UCN and ATS proteins during maintenance of planar growth in integuments.
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Affiliation(s)
- Balaji Enugutti
- Present address: Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3-5, 1030, Vienna, Austria
| | - Kay Schneitz
- Entwicklungsbiologie der Pflanzen, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Ramann-Strasse 4, 85354, Freising, Germany
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20
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Abstract
Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.
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Affiliation(s)
- Katina Lazarow
- Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, Germany
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21
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Paddock T, Lima D, Mason ME, Apel K, Armstrong GA. Arabidopsis light-dependent protochlorophyllide oxidoreductase A (PORA) is essential for normal plant growth and development. PLANT MOLECULAR BIOLOGY 2012; 78:447-60. [PMID: 22278767 DOI: 10.1007/s11103-012-9873-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 12/29/2011] [Indexed: 05/08/2023]
Abstract
During skotomorphogenesis in angiosperms, NADPH:protochlorophyllide oxidoreductase (POR) forms an aggregate of photolabile NADPH-POR-protochlorophyllide (Pchlide) ternary complexes localized to the prolamellar bodies within etioplasts. During photomorphogenesis, POR catalyzes the light-dependent reduction of Pchlide a to chlorophyllide (Chlide) a, which is subsequently converted to chlorophyll (Chl). In Arabidopsis there are three structurally related POR genes, denoted PORA, PORB and PORC. The PORA and PORB proteins accumulate during skotomorphogenesis. During illumination, PORA is only transiently expressed, whereas PORB and PORC persist and are responsible for bulk Chl synthesis throughout plant development. Here we have tested whether PORA is important for skotomorphogenesis by assisting in etioplast development, and normal photomorphogenic development. Using reverse genetic approaches, we have identified the porA-1 null mutant, which contains an insertion of the maize Dissociation transposable element in the PORA gene. Additionally, we have characterized PORA RNAi lines. The porA-1 and PORA RNAi lines display severe photoautotrophic growth defects, which can be partially rescued on sucrose-supplemented growth media. Elimination of PORA during skotomorphogenesis results in reductions in the volume and frequency of prolamellar bodies, and in photoactive Pchlide conversion. The porA-1 mutant characterization thus establishes a quantitative requirement for PORA in etioplast development by demonstrating significant membrane ultrastructural and biochemical defects, in addition to suggesting PORA-specific functions in photomorphogenesis and plant development.
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Affiliation(s)
- Troy Paddock
- Department of Plant Cellular and Molecular Biology, The Ohio State University, Columbus, OH 43210-1293, USA.
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22
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Ac/Ds-transposon activation tagging in poplar: a powerful tool for gene discovery. BMC Genomics 2012; 13:61. [PMID: 22309468 PMCID: PMC3295694 DOI: 10.1186/1471-2164-13-61] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 02/06/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Rapid improvements in the development of new sequencing technologies have led to the availability of genome sequences of more than 300 organisms today. Thanks to bioinformatic analyses, prediction of gene models and protein-coding transcripts has become feasible. Various reverse and forward genetics strategies have been followed to determine the functions of these gene models and regulatory sequences. Using T-DNA or transposons as tags, significant progress has been made by using "Knock-in" approaches ("gain-of-function" or "activation tagging") in different plant species but not in perennial plants species, e.g. long-lived trees. Here, large scale gene tagging resources are still lacking. RESULTS We describe the first application of an inducible transposon-based activation tagging system for a perennial plant species, as example a poplar hybrid (P. tremula L. × P. tremuloides Michx.). Four activation-tagged populations comprising a total of 12,083 individuals derived from 23 independent "Activation Tagging Ds" (ATDs) transgenic lines were produced and phenotyped. To date, 29 putative variants have been isolated and new ATDs genomic positions were successfully determined for 24 of those. Sequences obtained were blasted against the publicly available genome sequence of P. trichocarpa v2.0 (Phytozome v7.0; http://www.phytozome.net/poplar) revealing possible transcripts for 17 variants.In a second approach, 300 randomly selected individuals without any obvious phenotypic alterations were screened for ATDs excision. For one third of those transposition of ATDs was confirmed and in about 5% of these cases genes were tagged. CONCLUSIONS The novel strategy of first genotyping and then phenotyping a tagging population as proposed here is, in particular, applicable for long-lived, difficult to transform plant species. We could demonstrate the power of the ATDs transposon approach and the simplicity to induce ATDs transposition in vitro. Since a transposon is able to pass chromosomal boundaries, only very few primary transposon-carrying transgenic lines are required for the establishment of large transposon tagging populations. In contrast to T-DNA-based activation tagging, which is plagued by a lack of transformation efficiency and its time consuming nature, this for the first time, makes it feasible one day to tag (similarly to Arabidopsis) every gene within a perennial plant genome.
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23
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Imura Y, Kobayashi Y, Yamamoto S, Furutani M, Tasaka M, Abe M, Araki T. CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis. PLANT & CELL PHYSIOLOGY 2012; 53:287-303. [PMID: 22247249 PMCID: PMC3278046 DOI: 10.1093/pcp/pcs002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/05/2012] [Indexed: 05/22/2023]
Abstract
The proper timing of flowering is of crucial importance for reproductive success of plants. Regulation of flowering is orchestrated by inputs from both environmental and endogenous signals such as daylength, light quality, temperature and hormones, and key flowering regulators construct several parallel and interactive genetic pathways. This integrative regulatory network has been proposed to create robustness as well as plasticity of the regulation. Although knowledge of key genes and their regulation has been accumulated, there still remains much to learn about how they are organized into an integrative regulatory network. Here, we have analyzed the CRYPTIC PRECOCIOUS (CRP) gene for the Arabidopsis counterpart of the MED12 subunit of the Mediator. A novel dominant mutant, crp-1D, which causes up-regulation of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), FRUITFULL (FUL) and APETALA1 (AP1) expression in a FLOWERING LOCUS T (FT)-dependent manner, was identified in an enhancer screen of the early-flowering phenotype of 35S::FT. Genetic and molecular analysis of both crp-1D and crp loss-of-function alleles showed that MED12/CRP is required not only for proper regulation of SOC1, FUL and AP1, but also for up-regulation of FT, TWIN SISTER OF FT (TSF) and FD, and down-regulation of FLOWERING LOCUS C (FLC). These observations suggest that MED12/CRP is a novel flowering regulator with multiple regulatory target steps both upstream and downstream of the key flowering regulators including FT florigen. Our work, taken together with recent studies of other Mediator subunit genes, supports an emerging view that the Mediator plays multiple roles in the regulation of flowering.
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Affiliation(s)
- Yuri Imura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Yasushi Kobayashi
- Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Sumiko Yamamoto
- Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- Genome Informatics Laboratory, CIB-DDBJ, National Institute of Genetics, ROIS, Shizuoka, 411-8540 Japan
| | - Masahiko Furutani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0101 Japan
| | - Masao Tasaka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0101 Japan
| | - Mitsutomo Abe
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
- *Corresponding author: E-mail, ; Fax, +81-75-753-6470.
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24
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Wu J, Kong X, Wan J, Liu X, Zhang X, Guo X, Zhou R, Zhao G, Jing R, Fu X, Jia J. Dominant and pleiotropic effects of a GAI gene in wheat results from a lack of interaction between DELLA and GID1. PLANT PHYSIOLOGY 2011; 157:2120-30. [PMID: 22010107 PMCID: PMC3327208 DOI: 10.1104/pp.111.185272] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/12/2011] [Indexed: 05/18/2023]
Abstract
Dominance, semidominance, and recessiveness are important modes of Mendelian inheritance. The phytohormone gibberellin (GA) regulates many plant growth and developmental processes. The previously cloned semidominant GA-insensitive (GAI) genes Reduced height1 (Rht1) and Rht2 in wheat (Triticum aestivum) were the basis of the Green Revolution. However, no completely dominant GAI gene has been cloned. Here, we report the molecular characterization of Rht-B1c, a dominant GAI allele in wheat that confers more extreme characteristics than its incompletely dominant alleles. Rht-B1c is caused by a terminal repeat retrotransposons in miniature insertion in the DELLA domain. Yeast two-hybrid assays showed that Rht-B1c protein fails to interact with GA-INSENSITIVE DWARF1 (GID1), thereby blocking GA responses and resulting in extreme dwarfism and pleiotropic effects. By contrast, Rht-B1b protein only reduces interaction with GID1. Furthermore, we analyzed its functions using near-isogenic lines and examined its molecular mechanisms in transgenic rice. These results indicated that the affinity between GID1 and DELLA proteins is key to regulation of the stability of DELLA proteins, and differential interactions determine dominant and semidominant gene responses to GA.
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25
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Singh S, Tan HQ, Singh J. Mutagenesis of barley malting quality QTLs with Ds transposons. Funct Integr Genomics 2011; 12:131-41. [DOI: 10.1007/s10142-011-0258-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 10/25/2011] [Accepted: 11/02/2011] [Indexed: 11/28/2022]
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26
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Kim SR, Jeon JS, An G. Development of an efficient inverse PCR method for isolating gene tags from T-DNA insertional mutants in rice. Methods Mol Biol 2011; 678:139-46. [PMID: 20931378 DOI: 10.1007/978-1-60761-682-5_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The central goal of current genomics research in plants, as in other organisms, is to elucidate the functions of every gene. Insertional mutagenesis using known DNA sequences such as T-DNA is a powerful tool in functional genomics. Development of efficient methods for isolating the genomic sequences flanking insertion elements accelerates the systematic cataloging of insertional mutants, and thus allows functions to be assigned to uncharacterized genes via reverse genetic approaches. In our current study, we report a rapid and efficient inverse PCR (iPCR) method for the isolation of gene tags in T-DNA mutant lines of rice (Oryza sativa), a model monocot plant.
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Affiliation(s)
- Sung-Ryul Kim
- National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
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27
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Sun XD, Ni M. HYPOSENSITIVE TO LIGHT, an alpha/beta fold protein, acts downstream of ELONGATED HYPOCOTYL 5 to regulate seedling de-etiolation. MOLECULAR PLANT 2011; 4:116-26. [PMID: 20864454 DOI: 10.1093/mp/ssq055] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ambient light has profound effects on early seedling de-etiolation through red and far-red light-absorbing phytochromes and blue and UV-A light-absorbing cryptochromes. Subsequent integration of various light signal transduction pathways leads to changes in gene expression and morphogenic responses. Here, we report the isolation of a new Arabidopsis light-signaling component, HYPOSENSITIVE TO LIGHT or HTL. Both htl-1 and htl-2 alleles displayed a long hypocotyl phenotype under red, far-red, and blue light, whereas overexpression of HTL caused a short hypocotyl phenotype under similar light conditions. The mutants also showed other photomorphogenic defects such as elongated petioles, retarded cotyledon and leaf expansion, reduced accumulation of chlorophyll and anthocyanin pigments, and attenuated expression of light-responsive CHLOROPHYLL A/B BINDING PROTEIN 3 and CHALCONE SYNTHASE genes. HTL belongs to an alpha/beta fold protein family and is localized strongly in the nucleus and weakly in the cytosol. The expression of HTL was strongly induced by light of various wavelengths and this light induction was impaired in elongated hypocotyl 5. HY5 directly bound to both a C/G-box and a G-box in the HTL promoter but with a greater affinity toward the C/G-box. HTL, therefore, represents a new signaling step downstream of HY5 in phy- and cry-mediated de-etiolation responses.
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Affiliation(s)
- Xiao-Dong Sun
- Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
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28
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Wang P, Du Y, Li Y, Ren D, Song CP. Hydrogen peroxide-mediated activation of MAP kinase 6 modulates nitric oxide biosynthesis and signal transduction in Arabidopsis. THE PLANT CELL 2010; 22:2981-98. [PMID: 20870959 PMCID: PMC2965546 DOI: 10.1105/tpc.109.072959] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 08/26/2010] [Accepted: 09/10/2010] [Indexed: 05/17/2023]
Abstract
Nitric oxide (NO) is a bioactive molecule that functions in numerous physiological and developmental processes in plants, including lateral root development. In this study, we used biochemical and genetic approaches to analyze the function of Arabidopsis thaliana mitogen-activated protein kinase 6 (MPK6) in the regulation of NO synthesis in response to hydrogen peroxide (H₂O₂) during lateral root development. In both mpk6 mutants studied, H₂O₂-induced NO synthesis and nitrate reductase (NR) activity were decreased dramatically. Furthermore, one NR isoform, NIA2, was required for the MPK6-mediated production of NO induced by H₂O₂. Notably, NIA2 interacted physically with MPK6 in vitro and in vivo and also served as a substrate of MPK6. Phosphorylation of NIA2 by MPK6 led to an increase in NR activity, and Ser-627 was identified as the putative phosphorylation site on NIA2. Phenotypical analysis revealed that mpk6-2 and mpk6-3 seedlings produce more and longer lateral roots than wild-type plants did after application of the NO donor sodium nitroprusside or H₂O₂. These data support strongly a function of MPK6 in modulating NO production and signal transduction in response to H₂O₂ during Arabidopsis root development.
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Affiliation(s)
- Pengcheng Wang
- Laboratory of Plant Stress Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Yanyan Du
- Laboratory of Plant Stress Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Yuan Li
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Dongtao Ren
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Chun-Peng Song
- Laboratory of Plant Stress Biology, Department of Biology, Henan University, Kaifeng 475001, China
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29
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Talbot JC, Johnson SL, Kimmel CB. hand2 and Dlx genes specify dorsal, intermediate and ventral domains within zebrafish pharyngeal arches. Development 2010; 137:2507-17. [PMID: 20573696 PMCID: PMC2927700 DOI: 10.1242/dev.049700] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2010] [Indexed: 11/20/2022]
Abstract
The ventrally expressed secreted polypeptide endothelin1 (Edn1) patterns the skeleton derived from the first two pharyngeal arches into dorsal, intermediate and ventral domains. Edn1 activates expression of many genes, including hand2 and Dlx genes. We wanted to know how hand2/Dlx genes might generate distinct domain identities. Here, we show that differential expression of hand2 and Dlx genes delineates domain boundaries before and during cartilage morphogenesis. Knockdown of the broadly expressed genes dlx1a and dlx2a results in both dorsal and intermediate defects, whereas knockdown of three intermediate-domain restricted genes dlx3b, dlx4b and dlx5a results in intermediate-domain-specific defects. The ventrally expressed gene hand2 patterns ventral identity, in part by repressing dlx3b/4b/5a. The jaw joint is an intermediate-domain structure that expresses nkx3.2 and a more general joint marker, trps1. The jaw joint expression of trps1 and nkx3.2 requires dlx3b/4b/5a function, and expands in hand2 mutants. Both hand2 and dlx3b/4b/5a repress dorsal patterning markers. Collectively, our work indicates that the expression and function of hand2 and Dlx genes specify major patterning domains along the dorsoventral axis of zebrafish pharyngeal arches.
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30
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Li X, Lassner M, Zhang Y. Deleteagene: a fast neutron deletion mutagenesis-based gene knockout system for plants. Comp Funct Genomics 2010; 3:158-60. [PMID: 18628888 PMCID: PMC2447248 DOI: 10.1002/cfg.148] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2002] [Accepted: 01/30/2002] [Indexed: 11/06/2022] Open
Abstract
Deleteagene™ (Delete-a-gene) is a deletion-based gene knockout system for plants. To
obtain deletion mutants for a specific gene, random deletion libraries created by fast
neutron mutagenesis are screened by polymerase chain reaction (PCR) using primers
flanking the target gene. By adjusting the PCR extension time to preferentially amplify the
deletion alleles, deletion mutants can be identified in pools of DNA samples with each
sample representing more than a thousand mutant lines. In Arabidopsis, knockout plants
for greater than 80% of targeted genes have been obtained from a population of 51 840
lines. A large number of deletion mutants have been identified and multiple deletion alleles
are often recovered for targeted loci. In Arabidopsis, the method is very useful for
targeting small genes and can be used to find deletion mutants mutating two or three
tandem homologous genes. In addition, the method is demonstrated to be effective in rice
as a deletion mutant for a rice gene was obtained with a similar approach. Because fast
neutron mutagenesis is applicable to all plant genetic systems, Deleteagene™ has the potential to enable reverse genetics for a wide range of plant species.
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Affiliation(s)
- Xin Li
- Biotechnology Laboratory, 6174 University Blvd., University of British Columbia, BC V6T 1Z3, Canada
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31
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Blum R, Meyer KC, Wünschmann J, Lendzian KJ, Grill E. Cytosolic action of phytochelatin synthase. PLANT PHYSIOLOGY 2010; 153:159-69. [PMID: 20304971 PMCID: PMC2862410 DOI: 10.1104/pp.109.149922] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/15/2010] [Indexed: 05/20/2023]
Abstract
Glutathionylation of compounds is an important reaction in the detoxification of electrophilic xenobiotics and in the biosynthesis of endogenous molecules. The glutathione conjugates (GS conjugates) are further processed by peptidic cleavage reactions. In animals and plants, gamma-glutamyl transpeptidases initiate the turnover by removal of the glutamate residue from the conjugate. Plants have a second route leading to the formation of gamma-glutamylcysteinyl (gamma-GluCys) conjugates. Phytochelatin synthase (PCS) is well known to mediate the synthesis of heavy metal-binding phytochelatins. In addition, the enzyme is also able to catabolize GS conjugates to the gamma-GluCys derivative. In this study, we addressed the cellular compartmentalization of PCS and its role in the plant-specific gamma-GluCys conjugate pathway in Arabidopsis (Arabidopsis thaliana). Localization studies of both Arabidopsis PCS revealed a ubiquitous presence of AtPCS1 in Arabidopsis seedlings, while AtPCS2 was only detected in the root tip. A functional AtPCS1:eGFP (enhanced green fluorescent protein) fusion protein was localized to the cytosolic compartment. Inhibition of the vacuolar import of GS-bimane conjugate via azide treatment resulted in both a strong accumulation of gamma-GluCys-bimane and a massive increase of the cellular cysteine to GS-bimane ratio, which was not observed in PCS-deficient lines. These findings support a cytosolic action of PCS. Analysis of a triple mutant deficient in both Arabidopsis PCS and vacuolar gamma-glutamyl transpeptidase GGT4 is consistent with earlier observations of an efficient sequestration of GS conjugates into the vacuole and the requirement of GGT4 for their turnover. Hence, PCS contributes specifically to the cytosolic turnover of GS conjugates, and AtPCS1 plays the prominent role. We discuss a potential function of PCS in the cytosolic turnover of GS conjugates.
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32
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O'Malley RC, Ecker JR. Linking genotype to phenotype using the Arabidopsis unimutant collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:928-40. [PMID: 20409268 DOI: 10.1111/j.1365-313x.2010.04119.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The large collections of Arabidopsis thaliana sequence-indexed T-DNA insertion mutants are among the most important resources to emerge from the sequencing of the genome. Several laboratories around the world have used the Arabidopsis reference genome sequence to map T-DNA flanking sequence tags (FST) for over 325,000 T-DNA insertion lines. Over the past decade, phenotypes identified with T-DNA-induced mutants have played a critical role in advancing both basic and applied plant research. These widely used mutants are an invaluable tool for direct interrogation of gene function. However, most lines are hemizygous for the insertion, necessitating a genotyping step to identify homozygous plants for the quantification of phenotypes. This situation has limited the application of these collections for genome-wide screens. Isolating multiple homozygous insert lines for every gene in the genome would make it possible to systematically test the phenotypic consequence of gene loss under a wide variety of conditions. One major obstacle to achieving this goal is that 12% of genes have no insertion and 8% are only represented by a single allele. Generation of additional mutations to achieve full genome coverage has been slow and expensive since each insertion is sequenced one at a time. Recent advances in high-throughput sequencing technology open up a potentially faster and cost-effective means to create new, very large insertion mutant populations for plants or animals. With the combination of new tools for genome-wide studies and emerging phenotyping platforms, these sequence-indexed mutant collections are poised to have a larger impact on our understanding of gene function.
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Affiliation(s)
- Ronan C O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92307, USA
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Pavan S, Jacobsen E, Visser RGF, Bai Y. Loss of susceptibility as a novel breeding strategy for durable and broad-spectrum resistance. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2010; 25:1-12. [PMID: 20234841 PMCID: PMC2837247 DOI: 10.1007/s11032-009-9323-6] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 07/31/2009] [Indexed: 05/18/2023]
Abstract
Recent studies on plant immunity have suggested that a pathogen should suppress induced plant defense in order to infect a plant species, which otherwise would have been a nonhost to the pathogen. For this purpose, pathogens exploit effector molecules to interfere with different layers of plant defense responses. In this review, we summarize the latest findings on plant factors that are activated by pathogen effectors to suppress plant immunity. By looking from a different point of view into host and nonhost resistance, we propose a novel breeding strategy: disabling plant disease susceptibility genes (S-genes) to achieve durable and broad-spectrum resistance.
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Affiliation(s)
- Stefano Pavan
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Agroforestry, Environmental Biology and Chemistry, Section of Genetics and Plant Breeding, University of Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Evert Jacobsen
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. F. Visser
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Yuling Bai
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Qu S, Jeon JS, Ouwerkerk PBF, Bellizzi M, Leach J, Ronald P, Wang GL. Construction and application of efficient Ac-Ds transposon tagging vectors in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:982-992. [PMID: 19903220 DOI: 10.1111/j.1744-7909.2009.00870.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Transposons are effective mutagens alternative to T-DNA for the generation of insertional mutants in many plant species including those whose transformation is inefficient. The current strategies of transposon tagging are usually slow and labor-intensive and yield low frequency of tagged lines. We have constructed a series of transposon tagging vectors based on three approaches: (i) AcTPase controlled by glucocorticoid binding domain/VP16 acidic activation domain/Gal4 DNA-binding domain (GVG) chemical-inducible expression system; (ii) deletion of AcTPase via Cre-lox site-specific recombination that was initially triggered by Ds excision; and (iii) suppression of early transposition events in transformed rice callus through a dual-functional hygromycin resistance gene in a novel Ds element (HPT-Ds). We tested these vectors in transgenic rice and characterized the transposition events. Our results showed that these vectors are useful resources for functional genomics of rice and other crop plants. The vectors are freely available for the community.
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Affiliation(s)
- Shaohong Qu
- Department of Plant Pathology, Ohio State University, Columbus OH 43210, USA
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Rogers C, Wen J, Chen R, Oldroyd G. Deletion-based reverse genetics in Medicago truncatula. PLANT PHYSIOLOGY 2009; 151:1077-86. [PMID: 19759346 PMCID: PMC2773085 DOI: 10.1104/pp.109.142919] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 09/15/2009] [Indexed: 05/18/2023]
Abstract
The primary goal of reverse genetics, the identification of null mutations in targeted genes, is achieved through screening large populations of randomly mutagenized plants. T-DNA and transposon-based mutagenesis has been widely employed but is limited to species in which transformation and tissue culture are efficient. In other species, TILLING (for Targeting Induced Local Lesions IN Genomes), based on chemical mutagenesis, has provided an efficient method for the identification of single base pair mutations, only 5% of which will be null mutations. Furthermore, the efficiency of inducing point mutations, like insertion-based mutations, is dependent on target size. Here, we describe an alternative reverse genetic strategy based on physically induced genomic deletions that, independent of target size, exclusively recovers knockout mutants. Deletion TILLING (De-TILLING) employs fast neutron mutagenesis and a sensitive polymerase chain reaction-based detection. A population of 156,000 Medicago truncatula plants has been structured as 13 towers each representing 12,000 M2 plants. The De-TILLING strategy allows a single tower to be screened using just four polymerase chain reaction reactions. Dual screening and three-dimensional pooling allows efficient location of mutants from within the towers. With this method, we have demonstrated the detection of mutants from this population at a rate of 29% using five targets per gene. This De-TILLING reverse genetic strategy is independent of tissue culture and efficient plant transformation and therefore applicable to any plant species. De-TILLING mutants offer advantages for crop improvement as they possess relatively few background mutations and no exogenous DNA.
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Affiliation(s)
- Christian Rogers
- Department of Disease, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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Kondrychyn I, Garcia-Lecea M, Emelyanov A, Parinov S, Korzh V. Genome-wide analysis of Tol2 transposon reintegration in zebrafish. BMC Genomics 2009; 10:418. [PMID: 19737393 PMCID: PMC2753552 DOI: 10.1186/1471-2164-10-418] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 09/08/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Tol2, a member of the hAT family of transposons, has become a useful tool for genetic manipulation of model animals, but information about its interactions with vertebrate genomes is still limited. Furthermore, published reports on Tol2 have mainly been based on random integration of the transposon system after co-injection of a plasmid DNA harboring the transposon and a transposase mRNA. It is important to understand how Tol2 would behave upon activation after integration into the genome. RESULTS We performed a large-scale enhancer trap (ET) screen and generated 338 insertions of the Tol2 transposon-based ET cassette into the zebrafish genome. These insertions were generated by remobilizing the transposon from two different donor sites in two transgenic lines. We found that 39% of Tol2 insertions occurred in transcription units, mostly into introns. Analysis of the transposon target sites revealed no strict specificity at the DNA sequence level. However, Tol2 was prone to target AT-rich regions with weak palindromic consensus sequences centered at the insertion site. CONCLUSION Our systematic analysis of sequential remobilizations of the Tol2 transposon from two independent sites within a vertebrate genome has revealed properties such as a tendency to integrate into transcription units and into AT-rich palindrome-like sequences. This information will influence the development of various applications involving DNA transposons and Tol2 in particular.
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Affiliation(s)
- Igor Kondrychyn
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Singapore
| | - Marta Garcia-Lecea
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Singapore
| | - Alexander Emelyanov
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Singapore
- Temasek Life Sciences Laboratory, Singapore
| | - Sergey Parinov
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Singapore
- Temasek Life Sciences Laboratory, Singapore
| | - Vladimir Korzh
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
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Joshi V, Jander G. Arabidopsis methionine gamma-lyase is regulated according to isoleucine biosynthesis needs but plays a subordinate role to threonine deaminase. PLANT PHYSIOLOGY 2009; 151:367-78. [PMID: 19571310 PMCID: PMC2735994 DOI: 10.1104/pp.109.138651] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 06/22/2009] [Indexed: 05/19/2023]
Abstract
The canonical pathway for isoleucine biosynthesis in plants begins with the conversion of threonine to 2-ketobutyrate by threonine deaminase (OMR1). However, demonstration of methionine gamma-lyase (MGL) activity in Arabidopsis (Arabidopsis thaliana) suggested that production of 2-ketobutyrate from methionine can also lead to isoleucine biosynthesis. Rescue of the isoleucine deficit in a threonine deaminase mutant by MGL overexpression, as well as decreased transcription of endogenous Arabidopsis MGL in a feedback-insensitive threonine deaminase mutant background, shows that these two enzymes have overlapping functions in amino acid biosynthesis. In mgl mutant flowers and seeds, methionine levels are significantly increased and incorporation of [(13)C]Met into isoleucine is decreased, but isoleucine levels are unaffected. Accumulation of free isoleucine and other branched-chain amino acids is greatly elevated in response to drought stress in Arabidopsis. Gene expression analyses, amino acid phenotypes, and labeled precursor feeding experiments demonstrate that MGL activity is up-regulated by osmotic stress but likely plays a less prominent role in isoleucine biosynthesis than threonine deaminase. The observation that MGL makes a significant contribution to methionine degradation, particularly in reproductive tissue, suggests practical applications for silencing the expression of MGL in crop plants and thereby increasing the abundance of methionine, a limiting essential amino acid.
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Affiliation(s)
- Vijay Joshi
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
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Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M. Phenome analysis in plant species using loss-of-function and gain-of-function mutants. PLANT & CELL PHYSIOLOGY 2009; 50:1215-31. [PMID: 19502383 PMCID: PMC2709550 DOI: 10.1093/pcp/pcp078] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 05/29/2009] [Indexed: 05/20/2023]
Abstract
Analysis of genetic mutations is one of the most effective ways to investigate gene function. We now have methods that allow for mass production of mutant lines and cells in a variety of model species. Recently, large numbers of mutant lines have been generated by both 'loss-of-function' and 'gain-of-function' techniques. In parallel, phenotypic information covering various mutant resources has been acquired and released in web-based databases. As a result, significant progress in comprehensive phenotype analysis is being made through the use of these tools. Arabidopsis and rice are two major model plant species in which genome sequencing projects have been completed. Arabidopsis is the most widely used experimental plant, with a large number of mutant resources and several examples of systematic phenotype analysis. Rice is a major crop species and is used as a model plant, with an increasing number of mutant resources. Other plant species are also being employed in functional genetics research. In this review, the present status of mutant resources for large-scale studies of gene function in plant research and the current perspective on using loss-of-function and gain-of-function mutants in phenome research will be discussed.
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Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Shinya Takahashi
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510 Japan
| | - Youichi Kondou
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Minami Matsui
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- *Corresponding author: E-mail, ; Fax, +81-45-503-9584
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Randhawa HS, Singh J, Lemaux PG, Gill KS. Mapping barleyDsinsertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates. Genome 2009; 52:566-75. [DOI: 10.1139/g09-029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gene distribution is highly uneven in the large genomes of barley and wheat; however, location, order, and gene density of gene-containing regions are very similar between the two genomes. Flanking sequences from 35 unique, single-copy, barley Ds insertion events were physically mapped using wheat nullisomic-tetrasomic, ditelosomic, and deletion lines. Of the 35 sequences, 23 (66%) detected 34 loci mapping on all 7 homoeologous wheat groups. Seven sequences were not mapped owing to lack of polymorphism and the remaining 5 (14%) were barley-specific. All 34 loci physically mapped to the previously identified gene-rich regions (GRRs) of wheat, making the contained genes candidates for targeted mutagenesis by remobilization. Transpositions occurred preferentially into GRRs with higher recombination rates. The GRRs containing 17 of the 23 Ds insertions accounted for 60%–89% of the respective arm’s recombination. The remaining 6 (17%) insertions mapped to GRRs with <15% of the arm’s recombination. Overall, kb/cM estimates for the Ds-containing GRRs were twofold higher than those for regions without insertions. These results suggest that all genes may be targeted by transposon-based gene cloning, although the transposition frequency for genes present in recombination-poor regions is significantly less than that present in highly recombinogenic regions.
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Affiliation(s)
- Harpinder S. Randhawa
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Jaswinder Singh
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Peggy G. Lemaux
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
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Burgess HA, Johnson SL, Granato M. Unidirectional startle responses and disrupted left-right co-ordination of motor behaviors in robo3 mutant zebrafish. GENES BRAIN AND BEHAVIOR 2009; 8:500-11. [PMID: 19496826 DOI: 10.1111/j.1601-183x.2009.00499.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Roundabout (Robo) family of receptors and their Slit ligands play well-established roles in axonal guidance, including in humans where horizontal gaze palsy with progressive scoliosis (HGPPS) is caused by mutations in the robo3 gene. Although significant progress has been made toward understanding the mechanism by which Robo receptors establish commissural projections in the central nervous system, less is known about how these projections contribute to neural circuits mediating behavior. In this study, we report cloning of the zebrafish behavioral mutant twitch twice and show that twitch twice encodes robo3. We show that in mutant hindbrains the axons of an identified pair of neurons, the Mauthner cells, fail to cross the midline. The Mauthner neurons are essential for the startle response, and in twitch twice/robo3 mutants misguidance of the Mauthner axons results in a unidirectional startle response. Moreover, we show that twitch twice mutants exhibit normal visual acuity but display defects in horizontal eye movements, suggesting a specific and critical role for twitch twice/robo3 in sensory-guided behavior.
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Affiliation(s)
- H A Burgess
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6058, USA
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Skinner DJ, Gasser CS. Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants. BMC PLANT BIOLOGY 2009; 9:29. [PMID: 19291320 PMCID: PMC2664812 DOI: 10.1186/1471-2229-9-29] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 03/16/2009] [Indexed: 05/05/2023]
Abstract
BACKGROUND Arabidopsis ovules comprise four morphologically distinct parts: the nucellus, which contains the embryo sac, two integuments that become the seed coat, and the funiculus that anchors the ovule within the carpel. Analysis of developmental mutants has shown that ovule morphogenesis relies on tightly regulated genetic interactions that can serve as a model for developmental regulation. Redundancy, pleiotropic effects and subtle phenotypes may preclude identification of mutants affecting some processes in screens for phenotypic changes. Expression-based gene discovery can be used access such obscured genes. RESULTS Affymetrix microarrays were used for expression-based gene discovery to identify sets of genes expressed in either or both integuments. The genes were identified by comparison of pistil mRNA from wild type with mRNA from two mutants; inner no outer (ino, which lacks the outer integument), and aintegumenta (ant, which lacks both integuments). Pools of pistils representing early and late stages of ovule development were evaluated and data from the three genotypes were used to designate genes that were predominantly expressed in the integuments using pair-wise and cluster analyses. Approximately two hundred genes were found to have a high probability of preferential expression in these structures, and the predictive nature of the expression classes was confirmed with reverse transcriptase polymerase chain reaction and in situ hybridization. CONCLUSION The results showed that it was possible to use a mutant, ant, with broad effects on plant phenotype to identify genes expressed specifically in ovules, when coupled with predictions from known gene expression patterns, or in combination with a more specific mutant, ino. Robust microarray averaging (RMA) analysis of array data provided the most reliable comparisons, especially for weakly expressed genes. The studies yielded an over-abundance of transcriptional regulators in the identified genes, and these form a set of candidate genes for evaluation of roles in ovule development using reverse genetics.
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Affiliation(s)
- Debra J Skinner
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
- Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
| | - Charles S Gasser
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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Lazarow K, Lütticke S. An Ac/Ds-mediated gene trap system for functional genomics in barley. BMC Genomics 2009; 10:55. [PMID: 19178688 PMCID: PMC2647555 DOI: 10.1186/1471-2164-10-55] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 01/29/2009] [Indexed: 01/17/2023] Open
Abstract
Background Gene trapping is a powerful tool for gene discovery and functional genomics in both animals and plants. Upon insertion of the gene trap construct into an expressed gene, splice donor and acceptor sites facilitate the generation of transcriptional fusions between the flanking sequence and the reporter. Consequently, detection of reporter gene expression allows the identification of genes based on their expression pattern. Up to now rice is the only cereal crop for which gene trap approaches exist. In this study we describe a gene trap system in barley (Hordeum vulgare L.) based on the maize transposable elements Ac/Ds. Results We generated gene trap barley lines by crossing Ac transposase expressing plants with multiple independent transformants carrying the Ds based gene trap construct GTDsB. Upstream of the β-Glucuronidase start codon GTDsB carries splice donor and acceptor sites optimized for monocotyledonous plants. DNA blot analysis revealed GTDsB transposition frequencies of 11% and 26% in the F1 and F2 generation of gene trap lines and perpetuation of transposition activity in later generations. Furthermore, analysis of sequences flanking transposed GTDsB elements evidenced preferential insertion into expressed regions of the barley genome. We screened leaves, nodes, immature florets, pollinated florets, immature grains and seedlings of F2 plants and detected GUS expression in 51% (72/141) of the plants. Thus, reporter gene expression was found in 24 of the 28 F1 lines tested and in progeny of all GTDsB parental lines. Conclusion Due to the frequent transposition of GTDsB and the efficient expression of the GUS reporter gene, we conclude that this Ac/Ds-based gene trap system is an applicable approach for gene discovery in barley. The successful introduction of a gene trap construct optimized for monocots in barley contributes a novel functional genomics tool for this cereal crop.
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Affiliation(s)
- Katina Lazarow
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany.
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Wan S, Wu J, Zhang Z, Sun X, Lv Y, Gao C, Ning Y, Ma J, Guo Y, Zhang Q, Zheng X, Zhang C, Ma Z, Lu T. Activation tagging, an efficient tool for functional analysis of the rice genome. PLANT MOLECULAR BIOLOGY 2009; 69:69-80. [PMID: 18830797 DOI: 10.1007/s11103-008-9406-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 09/17/2008] [Indexed: 05/19/2023]
Abstract
Over the past 6 years, we have generated about 50,000 individual transgenic rice plants by an Agrobacterium-mediated transformation approach with the pER38 activation tagging vector. The vector contains tandemly arranged double 35S enhancers next to the right border of T-DNA. Expression analysis by reverse transcription-PCR indicates that the activation efficiency is high if the genes are located within 7 kb of the inserted double 35S enhancers. Comparative field phenotyping of part of the activation tagging and enhancer trapping populations in two generations (6,000 and 6,400 lines, respectively, in the T(0) generation, and 36,000 and 32,000 lines, respectively, in the T(1) generation) identified about four hundred dominant mutants. Characterization of a dominant mutant with a large leaf angle (M107) suggests that this mutant phenotype is caused by enhanced expression of CYP724B1/D11. The activation tagging pool described in this paper is a valuable alternative tool for functional analysis of the rice genome.
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Affiliation(s)
- Shuyan Wan
- Biotechnology Research Institute/National Key Facility for Gene Resources and Gene Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Ulker B, Peiter E, Dixon DP, Moffat C, Capper R, Bouché N, Edwards R, Sanders D, Knight H, Knight MR. Getting the most out of publicly available T-DNA insertion lines. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:665-77. [PMID: 18644000 DOI: 10.1111/j.1365-313x.2008.03608.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the course of several different projects, we came to realize that there is a significant amount of untapped potential in the publicly available T-DNA insertion lines. In addition to the GABI-Kat lines, which were designed specifically for activation tagging, lines from the SAIL and FLAGdb collections are also useful for this purpose. As well as the 35S promoter chosen for activation tagging in GABI-Kat lines, we found that the 1'2' bidirectional promoter is capable of activating expression of flanking genomic sequences in both GABI-Kat and SAIL lines. Thus these lines have added potential for activation tagging. We also show that these lines are capable of generating antisense transcripts and so have the potential to be used for suppression (loss/reduction of function) studies. By virtue of weak terminator sequences in some T-DNA constructs, transcript read-through from selectable markers is also possible, which again has the potential to be exploited in activation/suppression studies. Finally, we show that, by selecting and characterizing lines in which the T-DNA insertions are present specifically within introns of a target gene, an allelic series of mutants with varying levels of reduced expression can be generated, due to differences in efficiency of intron splicing. Taken together, our analyses demonstrate that there is a wealth of untapped potential within existing insertion lines for studies on gene function, and the effective exploitation of these resources is discussed.
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MESH Headings
- Antisense Elements (Genetics)
- Arabidopsis/genetics
- DNA, Bacterial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Genetic Vectors
- Genome, Plant
- Mutagenesis, Insertional/methods
- Plants, Genetically Modified/genetics
- Promoter Regions, Genetic
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- Bekir Ulker
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
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Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz). Mol Genet Genomics 2008; 280:305-17. [DOI: 10.1007/s00438-008-0366-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 07/02/2008] [Indexed: 11/28/2022]
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Knoth C, Eulgem T. The oomycete response gene LURP1 is required for defense against Hyaloperonospora parasitica in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:53-64. [PMID: 18346188 DOI: 10.1111/j.1365-313x.2008.03486.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
LURP1 is a member of the LURP cluster and the PR1 regulon, two previously defined sets of co-expressed Arabidopsis thaliana genes that share a pronounced upregulation in response to infections by the pathogenic oomycete Hyaloperonospora parasitica. LURP1 shows the most extreme transcriptional inducibility by H. parasitica of all LURP and PR1 regulon genes. Using insertion mutants we found that LURP1 is required for full basal defense to H. parasitica and resistance to this pathogen mediated by the R-proteins RPP4 and RPP5. The LURP1 protein shows no obvious similarity to proteins of known molecular function. We identified a 39-bp region of the LURP1 promoter that mediates reporter gene expression in response to H. parasitica and salicylic acid. This promoter region contains a W box motif, W(LURP1), that interacts in vitro with nuclear factors producing two separate DNA-binding patterns. W(LURP1)-related sequences are strongly enriched in the promoters of the PR1 regulon, suggesting a role for this motif in the coordinated expression of genes inducible by H. parasitica and related defense conditions.
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Affiliation(s)
- Colleen Knoth
- ChemGen IGERT Program, Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California at Riverside, CA 92521, USA
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Tanimoto M, Tremblay R, Colasanti J. Altered gravitropic response, amyloplast sedimentation and circumnutation in the Arabidopsis shoot gravitropism 5 mutant are associated with reduced starch levels. PLANT MOLECULAR BIOLOGY 2008; 67:57-69. [PMID: 18259878 DOI: 10.1007/s11103-008-9301-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 01/17/2008] [Indexed: 05/23/2023]
Abstract
Plants have developed sophisticated gravity sensing mechanisms to interpret environmental signals that are vital for optimum plant growth. Loss of SHOOT GRAVITROPISM 5 (SGR5) gene function has been shown to affect the gravitropic response of Arabidopsis inflorescence stems. SGR5 is a member of the INDETERMINATE DOMAIN (IDD) zinc finger protein family of putative transcription factors. As part of an ongoing functional analysis of Arabidopsis IDD genes (AtIDD) we have extended the characterisation of SGR5, and show that gravity sensing amyloplasts in the shoot endodermis of sgr5 mutants sediment more slowly than wild type, suggesting a defect in gravity perception. This is correlated with lower amyloplast starch levels, which may account for the reduced gravitropic sensitivity in sgr5. Further, we find that sgr5 mutants have a severely attenuated stem circumnutation movement typified by a reduced amplitude and an decreased periodicity. adg1-1 and sex1-1 mutants, which contain no starch or increased starch, respectively, also show alterations in the amplitude and period of circumnutation. Together these results suggest that plant growth movement may depend on starch levels and/or gravity sensing. Overall, we propose that loss of SGR5 regulatory activity affects starch accumulation in Arabidopsis shoot tissues and causes decreased sensitivity to gravity and diminished circumnutational movements.
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Affiliation(s)
- Mimi Tanimoto
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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Galbiati M, Simoni L, Pavesi G, Cominelli E, Francia P, Vavasseur A, Nelson T, Bevan M, Tonelli C. Gene trap lines identify Arabidopsis genes expressed in stomatal guard cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:750-62. [PMID: 18036199 DOI: 10.1111/j.1365-313x.2007.03371.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We employed a gene trap approach to identify genes expressed in stomatal guard cells of Arabidopsis thaliana. We examined patterns of reporter gene expression in approximately 20,000 gene trap lines, and recovered five lines with exclusive or preferential expression in stomata. The screen yielded two insertions in annotated genes, encoding the CYTOCHROME P450 86A2 (CYP86A2) mono-oxygenase, and the PLEIOTROPIC DRUG RESISTANCE 3 (AtPDR3) transporter. Expression of the trapped genes in guard cells was confirmed by RT-PCR experiments in purified stomata. Examination of homozygous mutant lines revealed that abscisic acid (ABA)-induced stomatal closure was impaired in the atpdr3 mutant. In three lines, insertions occurred outside transcribed units. Expression analysis of the genes surrounding the trapping inserts identified two genes selectively expressed in guard cells, corresponding to a PP2C PROTEIN PHOSPHATASE and an unknown expressed protein gene. Statistical analyses of the chromosomal regions tagged by the gene trap insertions revealed an over-represented [A/T]AAAG motif, previously described as an essential cis-active element for gene expression in stomata. The lines described in this work identify novel genes involved in the modulation of stomatal activity, provide useful markers for the study of developmental pathways in guard cells, and are a valuable source of guard cell-specific promoters.
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Affiliation(s)
- Massimo Galbiati
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20 133 Milano, Italy.
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Godge MR, Purkayastha A, Dasgupta I, Kumar PP. Virus-induced gene silencing for functional analysis of selected genes. PLANT CELL REPORTS 2008; 27:209-19. [PMID: 17938933 DOI: 10.1007/s00299-007-0460-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 09/05/2007] [Accepted: 09/21/2007] [Indexed: 05/25/2023]
Abstract
Virus-induced gene silencing (VIGS) is a technology that exploits an RNA-mediated antiviral defense mechanism and has been shown to be of great potential in plant reverse genetics. Circumvention of plant transformation, methodological simplicity, robustness, and speedy results makes VIGS an attractive alternative instrument in functional genomics, even in a high throughput fashion. The system is well established in Nicotiana benthamiana, and efforts are being made to improve VIGS in other species, including monocots. Here, we discuss the issues specific to the application of VIGS technology to determine gene function, which has revealed the roles of a variety of genes in disease resistance, abiotic stress, cellular signaling and secondary metabolite biosynthesis.
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Affiliation(s)
- Mandar R Godge
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
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50
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Qu S, Desai A, Wing R, Sundaresan V. A versatile transposon-based activation tag vector system for functional genomics in cereals and other monocot plants. PLANT PHYSIOLOGY 2008; 146:189-99. [PMID: 17993541 PMCID: PMC2230568 DOI: 10.1104/pp.107.111427] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 10/30/2007] [Indexed: 05/19/2023]
Abstract
Transposon insertional mutagenesis is an effective alternative to T-DNA mutagenesis when transformation through tissue culture is inefficient as is the case for many crop species. When used as activation tags, transposons can be exploited to generate novel gain-of-function phenotypes without transformation and are of particular value in the study of polyploid plants where gene knockouts will not have phenotypes. We have developed an in cis-activation-tagging Ac-Ds transposon system in which a T-DNA vector carries a Dissociation (Ds) element containing 4x cauliflower mosaic virus enhancers along with the Activator (Ac) transposase gene. Stable Ds insertions were selected using green fluorescent protein and red fluorescent protein genes driven by promoters that are functional in maize (Zea mays) and rice (Oryza sativa). The system has been tested in rice, where 638 stable Ds insertions were selected from an initial set of 26 primary transformants. By analysis of 311 flanking sequences mapped to the rice genome, we could demonstrate the wide distribution of the elements over the rice chromosomes. Enhanced expression of rice genes adjacent to Ds insertions was detected in the insertion lines using semiquantitative reverse transcription-PCR method. The in cis-two-element vector system requires minimal number of primary transformants and eliminates the need for crossing, while the use of fluorescent markers instead of antibiotic or herbicide resistance increases the applicability to other plants and eliminates problems with escapes. Because Ac-Ds has been shown to transpose widely in the plant kingdom, the activation vector system developed in this study should be of utility more generally to other monocots.
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Affiliation(s)
- Shaohong Qu
- Section of Plant Biology , University of California, Davis, CA 95616, USA
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