201
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Plewka P, Thompson A, Szymanski M, Nuc P, Knop K, Rasinska A, Bialkowska A, Szweykowska-Kulinska Z, Karlowski WM, Jarmolowski A. A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis. RNA Biol 2018; 15:726-738. [PMID: 29561243 PMCID: PMC6152437 DOI: 10.1080/15476286.2018.1445404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Arabidopsis GUT15 RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed GUT15 transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and GUT15-tRF-F5, which are both encoded by the final intron in the GUT15 gene. The GUT15-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway. The GUT15-encoded tRNA-like sequence has an inhibiting effect on the splicing of its host intron. Moreover, we demonstrate that the canonical tRNA genes nested within introns do not affect the splicing patterns of their host protein-coding transcripts.
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Affiliation(s)
- Patrycja Plewka
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Agnieszka Thompson
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Maciej Szymanski
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Przemyslaw Nuc
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Katarzyna Knop
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Agnieszka Rasinska
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Aleksandra Bialkowska
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Zofia Szweykowska-Kulinska
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Wojciech M Karlowski
- b Department of Computational Biology , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
| | - Artur Jarmolowski
- a Department of Gene Expression , Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan , Poznan , Poland
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202
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Symplasmic Intercellular Communication through Plasmodesmata. PLANTS 2018; 7:plants7010023. [PMID: 29558398 PMCID: PMC5874612 DOI: 10.3390/plants7010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/17/2018] [Accepted: 03/17/2018] [Indexed: 12/21/2022]
Abstract
Communication between cells is an essential process for developing and maintaining multicellular collaboration during plant development and physiological adaptation in response to environmental stimuli. The intercellular movement of proteins and RNAs in addition to the movement of small nutrients or signaling molecules such as sugars and phytohormones has emerged as a novel mechanism of cell-to-cell signaling in plants. As a strategy for efficient intercellular communication and long-distance molecule movement, plants have evolved plant-specific symplasmic communication networks via plasmodesmata (PDs) and the phloem.
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203
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Scholz SS, Schmidt-Heck W, Guthke R, Furch ACU, Reichelt M, Gershenzon J, Oelmüller R. Verticillium dahliae-Arabidopsis Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales. Front Microbiol 2018; 9:217. [PMID: 29497409 PMCID: PMC5819561 DOI: 10.3389/fmicb.2018.00217] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/30/2018] [Indexed: 01/27/2023] Open
Abstract
Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 h induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense- and stress-responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. After 3 weeks, severe disease symptoms can be detected for wild-type plants while mutants impaired in jasmonate synthesis and perception perform much better. Thus, plant jasmonates have an important influence on the interaction, which is already visible at the mRNA level before hormone changes occur. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.
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Affiliation(s)
- Sandra S Scholz
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wolfgang Schmidt-Heck
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany
| | - Reinhard Guthke
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany
| | - Alexandra C U Furch
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
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204
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Abstract
A new report shows that the HY5 transcription factor moves from shoots to roots in plants, mediating light regulation of root growth and nitrate uptake. This finding offers not only a mechanistic insight into shoot-root communication, but also scope for increasing crop yields.
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Affiliation(s)
- Klaus Palme
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany.
| | - William Teale
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Dovzhenko
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
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205
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Abstract
The phloem plays a central role in transporting resources and signalling molecules from fully expanded leaves to provide precursors for, and to direct development of, heterotrophic organs located throughout the plant body. We review recent advances in understanding mechanisms regulating loading and unloading of resources into, and from, the phloem network; highlight unresolved questions regarding the physiological significance of the vast array of proteins and RNAs found in phloem saps; and evaluate proposed structure/function relationships considered to account for bulk flow of sap, sustained at high rates and over long distances, through the transport phloem.
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Affiliation(s)
- Johannes Liesche
- Biomass Energy Center for Arid and Semi-arid lands, Northwest A&F University, Yangling, China
- College of Life Science, Northwest A&F University, Yangling , China
| | - John Patrick
- Department of Biological Sciences, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, Australia
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206
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Pucker B, Holtgräwe D, Weisshaar B. Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Res Notes 2017; 10:667. [PMID: 29202864 PMCID: PMC5716242 DOI: 10.1186/s13104-017-2985-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/23/2017] [Indexed: 12/26/2022] Open
Abstract
Objective The Arabidopsis thaliana Niederzenz-1 genome sequence was recently published with an ab initio gene prediction. In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11. Results Incorporation of hints generated from Araport11 enabled the precise prediction of non-canonical splice sites. Manual inspection of RNA-Seq read mapping and RT-PCR were applied to validate the structural annotations of non-canonical splice sites. Predictions of untranslated regions were also updated by harnessing the potential of Araport11’s information, which was generated by using high coverage RNA-Seq data. The improved gene set of the Nd-1 genome assembly (GeneSet_Nd-1_v1.1) was evaluated via comparison to the initial gene prediction (GeneSet_Nd-1_v1.0) as well as against Araport11 for the Col-0 reference genome sequence. GeneSet_Nd-1_v1.1 contains previously missed non-canonical splice sites in 1256 genes. Reciprocal best hits for 24,527 (89.4%) of all nuclear Col-0 genes against the GeneSet_Nd-1_v1.1 indicate a high gene prediction quality. Electronic supplementary material The online version of this article (10.1186/s13104-017-2985-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Boas Pucker
- Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniela Holtgräwe
- Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Bernd Weisshaar
- Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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207
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Wang X, Chen Y, Thomas CL, Ding G, Xu P, Shi D, Grandke F, Jin K, Cai H, Xu F, Yi B, Broadley MR, Shi L. Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply. DNA Res 2017; 24:407-417. [PMID: 28430897 PMCID: PMC5737433 DOI: 10.1093/dnares/dsx013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/29/2017] [Indexed: 12/29/2022] Open
Abstract
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population. One peak single-nucleotide polymorphism region on A3 was associated with all root system architecture traits and co-localized with a quantitative trait locus for primary root length at low phosphorus. Two more single-nucleotide polymorphism peaks on A5 for root dry weight at low phosphorus were detected in both growth systems and co-localized with a quantitative trait locus for the same trait. The candidate genes identified on A3 form a haplotype ‘BnA3Hap’, that will be important for understanding the phosphorus/root system interaction and for the incorporation into Brassica napus breeding programs.
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Affiliation(s)
- Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanling Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Catherine L Thomas
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12?5RD, UK
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Dexu Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Fabian Grandke
- Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen 35392, Germany
| | - Kemo Jin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12?5RD, UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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208
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Puga MI, Rojas-Triana M, de Lorenzo L, Leyva A, Rubio V, Paz-Ares J. Novel signals in the regulation of Pi starvation responses in plants: facts and promises. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:40-49. [PMID: 28587933 DOI: 10.1016/j.pbi.2017.05.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/09/2017] [Accepted: 05/19/2017] [Indexed: 05/10/2023]
Abstract
Plants have evolved numerous adaptive developmental and metabolic responses to cope with growth in conditions of limited phosphate (Pi). Regulation of these Pi starvation responses (PSR) at the organism level involves not only cellular Pi perception in different organs, but also inter-organ communication of Pi levels via systemic signaling. Here we summarize recent discoveries on Pi starvation sensing and signaling, with special emphasis on structure-function studies that showed a role for inositol polyphosphates (InsP) as intracellular Pi signals, and on genomic studies that identified a large number of mRNAs with inter-organ mobility, which provide an immense source of potential systemic signals in the control of PSR and other responses.
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Affiliation(s)
- María Isabel Puga
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Mónica Rojas-Triana
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Antonio Leyva
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Vicente Rubio
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
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209
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Ufer G, Gertzmann A, Gasulla F, Röhrig H, Bartels D. Identification and characterization of the phosphatidic acid-binding A. thaliana phosphoprotein PLDrp1 that is regulated by PLDα1 in a stress-dependent manner. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:276-290. [PMID: 28755507 DOI: 10.1111/tpj.13651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/12/2017] [Accepted: 07/24/2017] [Indexed: 05/08/2023]
Abstract
Phospholipase D (PLD) and its cleavage product phosphatidic acid (PA) are crucial in plant stress-signalling. Although some targets of PLD and PA have been identified, the signalling pathway is still enigmatic. This study demonstrates that the phosphoprotein At5g39570, now called PLD-regulated protein1 (PLDrp1), from Arabidopsis thaliana is directly regulated by PLDα1. The protein PLDrp1 can be divided into two regions with distinct properties. The conserved N-terminal region specifically binds PA, while the repeat-rich C-terminal domain suggests interactions with RNAs. The expression of PLDrp1 depends on PLDα1 and the plant water status. Water stress triggers a pldα1-like phenotype in PLDrp1 mutants and induces the expression of PLDrp1 in pldα1 mutants. The regulation of PLDrp1 by PLDα1 and environmental stressors contributes to the understanding of the complex PLD regulatory network and presents a new member of the PA-signalling chain in plants.
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Affiliation(s)
- Guido Ufer
- Institute of Molecular Physiology and Biotechnology of Planta (IMBIO), University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Anke Gertzmann
- Institute of Molecular Physiology and Biotechnology of Planta (IMBIO), University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Francisco Gasulla
- Institute of Molecular Physiology and Biotechnology of Planta (IMBIO), University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Horst Röhrig
- Institute of Molecular Physiology and Biotechnology of Planta (IMBIO), University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Planta (IMBIO), University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
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210
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Tsutsui H, Notaguchi M. The Use of Grafting to Study Systemic Signaling in Plants. PLANT & CELL PHYSIOLOGY 2017; 58:1291-1301. [PMID: 28961994 DOI: 10.1093/pcp/pcx098] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/03/2023]
Abstract
Grafting has long been an important technique in agriculture. Nowadays, grafting is a widely used technique also to study systemic long-distance signaling in plants. Plants respond to their surrounding environment, and at that time many aspects of their physiology are regulated systemically; these start from local input signals and are followed by the transmission of information to the rest of the plant. For example, soil nutrient conditions, light/photoperiod, and biotic and abiotic stresses affect plants heterogeneously, and plants perceive such information in specific plant tissues or organs. Such environmental cues are crucial determinants of plant growth and development, and plants drastically change their morphology and physiology to adapt to various events in their life. Hitherto, intensive studies have been conducted to understand systemic signaling in plants, and grafting techniques have permitted advances in this field. The breakthrough technique of micrografting in Arabidopsis thaliana was established in 2002 and led to the development of molecular genetic tools in this field. Thereafter, various phenomena of systemic signaling have been identified at the molecular level, including nutrient fixation, flowering, circadian clock and defense against pathogens. The significance of grafting is that it can clarify the transmission of the stimulus and molecules. At present, many micro- and macromolecules have been identified as mobile signals, which are transported through plant vascular tissues to co-ordinate their physiology and development. In this review, we introduce the various grafting techniques that have been developed, we report on the recent advances in the field of plant systemic signaling where grafting techniques have been applied and provide insights for the future.
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Affiliation(s)
- Hiroki Tsutsui
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Michitaka Notaguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Japan Science and Technology Agency, PRESTO, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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211
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Ikeuchi M, Rhodes J. Latest Advances in Plant Development and Environmental Response: The Inaugural Cold Spring Harbor Asia Plant Biology Meeting in Japan. PLANT & CELL PHYSIOLOGY 2017; 58:1286-1290. [PMID: 28961991 DOI: 10.1093/pcp/pcx083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
With stunning ocean views over Osaka Bay, Awaji Island played host to the first Cold Spring Harbor Asia Plant Biology meeting in Japan. The meeting, 'Latest Advances in Plant Development and Environmental Response' (CSHAPB), provided a platform to promote scientific communication and collaboration in the pan-pacific region. The event welcomed almost 200 scientists from around the world to showcase their cutting-edge research. Exemplary speakers from diverse research fields presented their latest discoveries, ranging from developmental mechanisms to host-pathogen interactions, environmental responses and stress memory. Here we seek to review the meeting and highlight some of the salient themes that emerged over the course of the 3 d.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, 1-7-22 Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jack Rhodes
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
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212
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Exogenous Auxin Elicits Changes in the Arabidopsis thaliana Root Proteome in a Time-Dependent Manner. Proteomes 2017; 5:proteomes5030016. [PMID: 28698516 PMCID: PMC5620533 DOI: 10.3390/proteomes5030016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/27/2017] [Accepted: 07/04/2017] [Indexed: 11/24/2022] Open
Abstract
Auxin is involved in many aspects of root development and physiology, including the formation of lateral roots. Improving our understanding of how the auxin response is mediated at the protein level over time can aid in developing a more complete molecular framework of the process. This study evaluates the effects of exogenous auxin treatment on the Arabidopsis root proteome after exposure of young seedlings to auxin for 8, 12, and 24 h, a timeframe permitting the initiation and full maturation of individual lateral roots. Root protein extracts were processed to peptides, fractionated using off-line strong-cation exchange, and analyzed using ultra-performance liquid chromatography and data independent acquisition-based mass spectrometry. Protein abundances were then tabulated using label-free techniques and evaluated for significant changes. Approximately 2000 proteins were identified during the time course experiment, with the number of differences between the treated and control roots increasing over the 24 h time period, with more proteins found at higher abundance with exposure to auxin than at reduced abundance. Although the proteins identified and changing in levels at each time point represented similar biological processes, each time point represented a distinct snapshot of the response. Auxin coordinately regulates many physiological events in roots and does so by influencing the accumulation and loss of distinct proteins in a time-dependent manner. Data are available via ProteomeXchange with the identifier PXD001400.
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213
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Plötner B, Nurmi M, Fischer A, Watanabe M, Schneeberger K, Holm S, Vaid N, Schöttler MA, Walther D, Hoefgen R, Weigel D, Laitinen RAE. Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:251-262. [PMID: 28378460 DOI: 10.1111/tpj.13560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 05/28/2023]
Abstract
Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.
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Affiliation(s)
- Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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214
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Wang F, Deng M, Xu J, Zhu X, Mao C. Molecular mechanisms of phosphate transport and signaling in higher plants. Semin Cell Dev Biol 2017. [PMID: 28648582 DOI: 10.1016/j.semcdb.2017.06.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Phosphorus (P) is an essential macronutrient for plant growth and development. To adapt to low inorganic-phosphate (Pi) environments, plants have evolved complex mechanisms and pathways that regulate the acquisition and remobilization of Pi and maintain P homeostasis. These mechanisms are regulated by complex gene regulatory networks through the functions of Pi transporters (PTs) and Pi starvation-induced (PSI) genes. This review summarizes recent progress in determining the molecular regulatory mechanisms of phosphate transporters and the Pi signaling network in the dicot Arabidopsis (Arabidopsis thaliana) and the monocot rice (Oryza sativa L.). Recent advances in this field provide a reference for understanding plant Pi signaling and specific mechanisms that mediate plant adaptation to environments with limited Pi availability. We propose potential biotechnological applications of known genes to develop plant cultivars with improved Pi uptake and use efficiency.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Meiju Deng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xinlu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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215
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Kyriacou MC, Rouphael Y, Colla G, Zrenner R, Schwarz D. Vegetable Grafting: The Implications of a Growing Agronomic Imperative for Vegetable Fruit Quality and Nutritive Value. FRONTIERS IN PLANT SCIENCE 2017; 8:741. [PMID: 28553298 PMCID: PMC5427113 DOI: 10.3389/fpls.2017.00741] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/20/2017] [Indexed: 05/19/2023]
Abstract
Grafting has become an imperative for intensive vegetable production since chlorofluorocarbon-based soil fumigants were banned from use on grounds of environmental protection. Compelled by this development, research into rootstock-scion interaction has broadened the potential applications of grafting in the vegetable industry beyond aspects of soil phytopathology. Grafting has been increasingly tapped for cultivation under adverse environs posing abiotic and biotic stresses to vegetable crops, thus enabling expansion of commercial production onto otherwise under-exploited land. Vigorous rootstocks have been employed not only in the open field but also under protected cultivation where increase in productivity improves distribution of infrastructural and energy costs. Applications of grafting have expanded mainly in two families: the Cucurbitaceae and the Solanaceae, both of which comprise major vegetable crops. As the main drives behind the expansion of vegetable grafting have been the resistance to soilborne pathogens, tolerance to abiotic stresses and increase in yields, rootstock selection and breeding have accordingly conformed to the prevailing demand for improving productivity, arguably at the expense of fruit quality. It is, however, compelling to assess the qualitative implications of this growing agronomic practice for human nutrition. Problems of impaired vegetable fruit quality have not infrequently been associated with the practice of grafting. Accordingly, the aim of the current review is to reassess how the practice of grafting and the prevalence of particular types of commercial rootstocks influence vegetable fruit quality and, partly, storability. Physical, sensorial and bioactive aspects of quality are examined with respect to grafting for watermelon, melon, cucumber, tomato, eggplant, and pepper. The physiological mechanisms at play which mediate rootstock effects on scion performance are discussed in interpreting the implications of grafting for the configuration of vegetable fruit physicochemical quality and nutritive value.
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Affiliation(s)
- Marios C. Kyriacou
- Department of Vegetable Crops, Agricultural Research InstituteNicosia, Cyprus
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico IINaples, Italy
| | - Giuseppe Colla
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Rita Zrenner
- Leibniz Institute of Vegetable and Ornamental CropsGroßbeeren, Germany
| | - Dietmar Schwarz
- Leibniz Institute of Vegetable and Ornamental CropsGroßbeeren, Germany
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216
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Bellegarde F, Gojon A, Martin A. Signals and players in the transcriptional regulation of root responses by local and systemic N signaling in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2553-2565. [PMID: 28369491 DOI: 10.1093/jxb/erx062] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In natural environments, nitrogen (N) concentration in the soil fluctuates greatly and is often limiting for plant growth and development. The ability of plants to respond to changes in N availability is therefore essential for adaptation. The response of plants to N variations consists in particular of adjusting root N uptake systems and root architecture. To do so, plants integrate local sensing and signaling of external N availability with systemic sensing and signaling of their internal N status, in order to tune the functional and structural properties of the root system in accordance with the N demand for growth of the whole plant. Transcriptional regulation of gene expression is one of the most important processes plants use to adapt the properties of the root system in response to local and long-distance N pathways. This review focuses on the mechanisms that give rise to transcriptional responses in Arabidopsis roots under N fluctuations, with an emphasis on those associated with the regulation of nitrate uptake and transport systems. We discuss the putative long-distance signals triggering the gene expression responses, as well as the molecular players that locally induce transcriptional changes. We also highlight several observations revealing the importance of adopting an integrative approach in the regulation of N signaling.
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Affiliation(s)
- Fanny Bellegarde
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
| | - Alain Gojon
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
| | - Antoine Martin
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
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217
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Ostendorp A, Pahlow S, Krüßel L, Hanhart P, Garbe MY, Deke J, Giavalisco P, Kehr J. Functional analysis of Brassica napus phloem protein and ribonucleoprotein complexes. THE NEW PHYTOLOGIST 2017; 214:1188-1197. [PMID: 28052459 PMCID: PMC6079638 DOI: 10.1111/nph.14405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/26/2016] [Indexed: 05/18/2023]
Abstract
Phloem sap contains a large number of macromolecules, including proteins and RNAs from different classes. Proteome analyses of phloem samples from different plant species under denaturing conditions identified hundreds of proteins potentially involved in diverse processes. Surprisingly, these studies also found a significant number of ribosomal and proteasomal proteins. This led to the suggestion that active ribosome and proteasome complexes might be present in the phloem, challenging the paradigm that protein synthesis and turnover are absent from the enucleate sieve elements of angiosperms. However, the existence of such complexes has as yet not been demonstrated. In this study we used three-dimensional gel electrophoresis to separate several protein complexes from native phloem sap from Brassica napus. Matrix-assisted laser desorption ionization-time of flight MS analyses identified more than 100 proteins in the three major protein-containing complexes. All three complexes contained proteins belonging to different ribosomal fragments and blue native northern blot confirmed the existence of ribonucleoprotein complexes. In addition, one complex contained proteasome components and further functional analyses confirmed activity of a proteasomal degradation pathway and showed a large number of ubiquitinated phloem proteins. Our results suggest specialized roles for ubiquitin modification and proteasome-mediated degradation in the phloem.
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Affiliation(s)
- Anna Ostendorp
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
| | - Steffen Pahlow
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
| | - Lena Krüßel
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
| | - Patrizia Hanhart
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
| | - Marcel Y. Garbe
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
| | - Jennifer Deke
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiologyam Mühlenberg 1Potsdam14476Germany
| | - Julia Kehr
- Molecular Plant GeneticsUniversity HamburgBiocenter Klein Flottbek, Ohnhorststr. 18Hamburg22609Germany
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218
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Choi WG, Miller G, Wallace I, Harper J, Mittler R, Gilroy S. Orchestrating rapid long-distance signaling in plants with Ca 2+ , ROS and electrical signals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:698-707. [PMID: 28112437 PMCID: PMC5677518 DOI: 10.1111/tpj.13492] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/15/2017] [Accepted: 01/17/2017] [Indexed: 05/18/2023]
Abstract
Plants show a rapid systemic response to a wide range of environmental stresses, where the signals from the site of stimulus perception are transmitted to distal organs to elicit plant-wide responses. A wide range of signaling molecules are trafficked through the plant, but a trio of potentially interacting messengers, reactive oxygen species (ROS), Ca2+ and electrical signaling ('trio signaling') appear to form a network supporting rapid signal transmission. The molecular components underlying this rapid communication are beginning to be identified, such as the ROS producing NAPDH oxidase RBOHD, the ion channel two pore channel 1 (TPC1), and glutamate receptor-like channels GLR3.3 and GLR3.6. The plant cell wall presents a plant-specific route for possible propagation of signals from cell to cell. However, the degree to which the cell wall limits information exchange between cells via transfer of small molecules through an extracellular route, or whether it provides an environment to facilitate transmission of regulators such as ROS or H+ remains to be determined. Similarly, the role of plasmodesmata as both conduits and gatekeepers for the propagation of rapid cell-to-cell signaling remains a key open question. Regardless of how signals move from cell to cell, they help prepare distant parts of the plant for impending challenges from specific biotic or abiotic stresses.
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Affiliation(s)
- Won-Gyu Choi
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA
- For correspondence ( or )
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, The Gonda Medical Diagnostic Research Building (204), Room 211, Ramat-Gan 52900, Israel
| | - Ian Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA
| | - Jeffrey Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA
- For correspondence ( or )
| | - Ron Mittler
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
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219
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Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate. Proc Natl Acad Sci U S A 2017; 114:E3563-E3572. [PMID: 28400510 DOI: 10.1073/pnas.1701952114] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Low phosphate (Pi) availability constrains plant development and seed production in both natural and agricultural ecosystems. When Pi is scarce, modifications of root system architecture (RSA) enhance the soil exploration ability of the plant and lead to an increase in Pi uptake. In Arabidopsis, an iron-dependent mechanism reprograms primary root growth in response to low Pi availability. This program is activated upon contact of the root tip with low-Pi media and induces premature cell differentiation and the arrest of mitotic activity in the root apical meristem, resulting in a short-root phenotype. However, the mechanisms that regulate the primary root response to Pi-limiting conditions remain largely unknown. Here we report on the isolation and characterization of two low-Pi insensitive mutants (lpi5 and lpi6), which have a long-root phenotype when grown in low-Pi media. Cellular, genomic, and transcriptomic analysis of low-Pi insensitive mutants revealed that the genes previously shown to underlie Arabidopsis Al tolerance via root malate exudation, known as SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) and ALUMINUM ACTIVATED MALATE TRANSPORTER 1 (ALMT1), represent a critical checkpoint in the root developmental response to Pi starvation in Arabidopsis thaliana Our results also show that exogenous malate can rescue the long-root phenotype of lpi5 and lpi6 Malate exudation is required for the accumulation of Fe in the apoplast of meristematic cells, triggering the differentiation of meristematic cells in response to Pi deprivation.
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220
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Wang J, Jiang L, Wu R. Plant grafting: how genetic exchange promotes vascular reconnection. THE NEW PHYTOLOGIST 2017; 214:56-65. [PMID: 27991666 DOI: 10.1111/nph.14383] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/13/2016] [Indexed: 05/17/2023]
Abstract
Grafting has been widely used to improve horticultural traits. It has also served increasingly as a tool to investigate the long-distance transport of molecules that is an essential part for key biological processes. Many studies have revealed the molecular mechanisms of graft-induced phenotypic variation in anatomy, morphology and production. Here, we review the phenomena and their underlying mechanisms by which macromolecules, including RNA, protein, and even DNA, are transported between scions and rootstocks via vascular tissues. We further propose a conceptual framework that characterizes and quantifies the driving mechanisms of scion-rootstock interactions toward vascular reconnection and regeneration.
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Affiliation(s)
- Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA, 17033, USA
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221
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Abstract
The parasitic plant Cuscuta exchanges mRNAs with its hosts. Systemic mobility of mRNAs within plants is well documented, and has gained increasing attention as studies using grafted plant systems have revealed new aspects of mobile mRNA regulation and function. But parasitic plants take this phenomenon to a new level by forming seamless connections to a wide range of host species, and raising questions about how mRNAs might function after transfer to a different species. Cuscuta and other parasitic plant species also take siRNAs from their hosts, indicating that multiple types of RNA are capable of trans-specific movement. Parasitic plants are intriguing systems for studying RNA mobility, in part because such exchange opens new possibilities for control of parasitic weeds, but also because they provide a fresh perspective into understanding roles of RNAs in inter-organismal communication.
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Affiliation(s)
- James H Westwood
- a Department of Plant Pathology, Physiology and Weed Science , Virginia Tech , Blacksburg , VA , USA
| | - Gunjune Kim
- a Department of Plant Pathology, Physiology and Weed Science , Virginia Tech , Blacksburg , VA , USA
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222
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Hannapel DJ, Banerjee AK. Multiple Mobile mRNA Signals Regulate Tuber Development in Potato. PLANTS 2017; 6:plants6010008. [PMID: 28208608 PMCID: PMC5371767 DOI: 10.3390/plants6010008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/24/2017] [Accepted: 01/30/2017] [Indexed: 12/17/2022]
Abstract
Included among the many signals that traffic through the sieve element system are full-length mRNAs that function to respond to the environment and to regulate development. In potato, several mRNAs that encode transcription factors from the three-amino-loop-extension (TALE) superfamily move from leaves to roots and stolons via the phloem to control growth and signal the onset of tuber formation. This RNA transport is enhanced by short-day conditions and is facilitated by RNA-binding proteins from the polypyrimidine tract-binding family of proteins. Regulation of growth is mediated by three mobile mRNAs that arise from vasculature in the leaf. One mRNA, StBEL5, functions to activate growth, whereas two other, sequence-related StBEL's, StBEL11 and StBEL29, function antagonistically to repress StBEL5 target genes involved in promoting tuber development. This dynamic system utilizes closely-linked phloem-mobile mRNAs to control growth in developing potato tubers. In creating a complex signaling pathway, potato has evolved a long-distance transport system that regulates underground organ development through closely-associated, full-length mRNAs that function as either activators or repressors.
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Affiliation(s)
- David J Hannapel
- Plant Biology Major, 253 Horticulture Hall, Iowa State University, Ames, IA 50011-1100, USA.
| | - Anjan K Banerjee
- Biology Division, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
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223
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Schultz ER, Zupanska AK, Sng NJ, Paul AL, Ferl RJ. Skewing in Arabidopsis roots involves disparate environmental signaling pathways. BMC PLANT BIOLOGY 2017; 17:31. [PMID: 28143395 PMCID: PMC5286820 DOI: 10.1186/s12870-017-0975-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Skewing root patterns provide key insights into root growth strategies and mechanisms that produce root architectures. Roots exhibit skewing and waving when grown on a tilted, impenetrable surface. The genetics guiding these morphologies have been examined, revealing that some Arabidopsis ecotypes skew and wave (e.g. WS), while others skew insignificantly but still wave (e.g. Col-0). The underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing. RESULTS This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling. CONCLUSIONS This study identified 11 genes whose change in expression level is associated with root skewing behavior. These genes are involved in signaling and perception, rather than the physical restructuring of root. Future work is needed to elucidate the potential role of these candidate genes during root skewing.
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Affiliation(s)
- Eric R. Schultz
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611 USA
- Present address: Department of Biology, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Agata K. Zupanska
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611 USA
| | - Natasha J. Sng
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611 USA
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611 USA
| | - Robert J. Ferl
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611 USA
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610 USA
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224
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Abstract
The translationally controlled tumor protein (TCTP) is a small, multifunctional protein found in most, if not all, eukaryotic lineages, involved in a myriad of key regulatory processes. Among these, the control of proliferation and inhibition of cell death, as well as differentiation, are the most important, and it is probable that other responses are derived from the ability of TCTP to influence them in both unicellular and multicellular organisms. In the latter, an additional function for TCTP stems from its capacity to be secreted via a nonclassical pathway and function in a non-cell autonomous (paracrine) manner, thus affecting the responses of neighboring or distant cells to developmental or environmental stimuli (as in the case of serum TCTP/histamine-releasing factor in mammals and phloem TCTP in Arabidopsis). The additional ability to traverse membranes without a requirement for transmembrane receptors adds to its functional flexibility. The long-distance transport of TCTP mRNA and protein in plants via the vascular system supports the notion that an important aspect of TCTP function is its ability to influence the response of neighboring and distant cells to endogenous and exogenous signals in a supracellular manner. The predicted tridimensional structure of TCTPs indicates a high degree of conservation, more than its amino acid sequence similarity could suggest. However, subtle differences in structure could lead to different activities, as evidenced by TCTPs secreted by Plasmodium spp. Similar structural variations in animal and plant TCTPs, likely the result of convergent evolution, could lead to deviations from the canonical function of this group of proteins, which could have an impact from a biomedical and agricultural perspectives.
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Affiliation(s)
| | - Roberto Ruiz-Medrano
- Department of Biotechnology and Bioengineering, Center for Research and Advanced Studies of the National Polytechnic Institute, Avenida IPN 2508, Colonia San Pedro Zacatenco, México City, 07360, México.
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225
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Abstract
Multipartite viruses have one of the most puzzling genetic organizations found in living organisms. These viruses have several genome segments, each containing only a part of the genetic information, and each individually encapsidated into a separate virus particle. While countless studies on molecular and cellular mechanisms of the infection cycle of multipartite viruses are available, just as for other virus types, very seldom is their lifestyle questioned at the viral system level. Moreover, the rare available “system” studies are purely theoretical, and their predictions on the putative benefit/cost balance of this peculiar genetic organization have not received experimental support. In light of ongoing progresses in general virology, we here challenge the current hypotheses explaining the evolutionary success of multipartite viruses and emphasize their shortcomings. We also discuss alternative ideas and research avenues to be explored in the future in order to solve the long-standing mystery of how viral systems composed of interdependent but physically separated information units can actually be functional.
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226
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Guan D, Yan B, Thieme C, Hua J, Zhu H, Boheler KR, Zhao Z, Kragler F, Xia Y, Zhang S. PlaMoM: a comprehensive database compiles plant mobile macromolecules. Nucleic Acids Res 2016; 45:D1021-D1028. [PMID: 27924044 PMCID: PMC5210661 DOI: 10.1093/nar/gkw988] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/23/2016] [Accepted: 10/13/2016] [Indexed: 01/14/2023] Open
Abstract
In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein–protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/.
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Affiliation(s)
- Daogang Guan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.,School of Biomedical Sciences, The University of Hong Kong, Hong Kong.,Laboratory for Food Safety and Environmental Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Bin Yan
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong.,Partner State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong
| | - Christoph Thieme
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong
| | - Jingmin Hua
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Hailong Zhu
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong.,Laboratory for Food Safety and Environmental Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | | | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Friedrich Kragler
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong .,Max Planck Institute of Molecular Plant Physiology Am Mühlenberg 1,14476 Potsdam-Golm, Germany
| | - Shoudong Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
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227
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Figueroa-Yañez L, Pereira-Santana A, Arroyo-Herrera A, Rodriguez-Corona U, Sanchez-Teyer F, Espadas-Alcocer J, Espadas-Gil F, Barredo-Pool F, Castaño E, Rodriguez-Zapata LC. RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PLoS One 2016; 11:e0165030. [PMID: 27764197 PMCID: PMC5072549 DOI: 10.1371/journal.pone.0165030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/05/2016] [Indexed: 11/18/2022] Open
Abstract
Plants respond to stress through metabolic and morphological changes that increase their ability to survive and grow. To this end, several transcription factor families are responsible for transmitting the signals that are required for these changes. Here, we studied the transcription factor superfamily AP2/ERF, particularly, RAP2.4 from Carica papaya cv. Maradol. We isolated four genes (CpRap2.4a, CpRAap2.4b, CpRap2.1 and CpRap2.10), and an in silico analysis showed that the four genes encode proteins that contain a conserved APETALA2 (AP2) domain located within group I and II transcription factors of the AP2/ERF superfamily. Semiquantitative PCR experiments indicated that each CpRap2 gene is differentially expressed under stress conditions, such as extreme temperatures. Moreover, genetic transformants of tobacco plants overexpressing CpRap2.4a and CpRap2.4b genes show a high level of tolerance to cold and heat stress compared to non-transformed plants. Confocal microscopy analysis of tobacco transgenic plants showed that CpRAP2.4a and CpRAP2.4b proteins were mainly localized to the nuclei of cells from the leaves and roots and also in the sieve elements. Moreover, the movement of CpRap2.4a RNA in tobacco grafting was analyzed. Our results indicate that CpRap2.4a and CpRap2.4b RNA in the papaya tree have a functional role in the response to stress conditions such as exposure to extreme temperatures via direct translation outside the parental RNA cell.
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Affiliation(s)
- Luis Figueroa-Yañez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | | | - Ana Arroyo-Herrera
- Laboratorio de Farmacología, Facultad de Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Ulises Rodriguez-Corona
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Felipe Sanchez-Teyer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Jorge Espadas-Alcocer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Francisco Espadas-Gil
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Felipe Barredo-Pool
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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Figueroa-Yañez L, Pereira-Santana A, Arroyo-Herrera A, Rodriguez-Corona U, Sanchez-Teyer F, Espadas-Alcocer J, Espadas-Gil F, Barredo-Pool F, Castaño E, Rodriguez-Zapata LC. RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PLoS One 2016; 11:e0165030. [DOI: https:/doi.org/10.1371/journal.pone.0165030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
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229
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Rabiger DS, Taylor JM, Spriggs A, Hand ML, Henderson ST, Johnson SD, Oelkers K, Hrmova M, Saito K, Suzuki G, Mukai Y, Carroll BJ, Koltunow AMG. Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation. BMC Biol 2016; 14:86. [PMID: 27716180 PMCID: PMC5054587 DOI: 10.1186/s12915-016-0311-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
Background Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts. Results A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified. Conclusions The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David S Rabiger
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Melanie L Hand
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Steven T Henderson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Karsten Oelkers
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, University of Adelaide PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Keisuke Saito
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Anna M G Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
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Yuen CYL, Shek R, Kang BH, Matsumoto K, Cho EJ, Christopher DA. Arabidopsis protein disulfide isomerase-8 is a type I endoplasmic reticulum transmembrane protein with thiol-disulfide oxidase activity. BMC PLANT BIOLOGY 2016; 16:181. [PMID: 27549196 PMCID: PMC4994283 DOI: 10.1186/s12870-016-0869-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/08/2016] [Indexed: 05/26/2023]
Abstract
BACKGROUND In eukaryotes, classical protein disulfide isomerases (PDIs) facilitate the oxidative folding of nascent secretory proteins in the endoplasmic reticulum by catalyzing the formation, breakage, and rearrangement of disulfide bonds. Terrestrial plants encode six structurally distinct subfamilies of PDIs. The novel PDI-B subfamily is unique to terrestrial plants, and in Arabidopsis is represented by a single member, PDI8. Unlike classical PDIs, which lack transmembrane domains (TMDs), PDI8 is unique in that it has a C-terminal TMD and a single N-terminal thioredoxin domain (instead of two). No PDI8 isoforms have been experimentally characterized to date. Here we describe the characterization of the membrane orientation, expression, sub-cellular localization, and biochemical function of this novel member of the PDI family. RESULTS Histochemical staining of plants harboring a PDI8 promoter:β-glucuronidase (GUS) fusion revealed that the PDI8 promoter is highly active in young, expanding leaves, the guard cells of cotyledons, and in the vasculature of several organs, including roots, leaves, cotyledons, and flowers. Immunoelectron microscopy studies using a PDI8-specific antibody on root and shoot apical cells revealed that PDI8 localizes to the endoplasmic reticulum (ER). Transient expression of two PDI8 fusions to green fluorescent protein (spGFP-PDI8 and PDI8-GFP-KKED) in leaf mesophyll protoplasts also resulted in labeling of the ER. Protease-protection immunoblot analysis indicated that PDI8 is a type I membrane protein, with its catalytic domain facing the ER lumen. The lumenal portion of PDI8 was able to functionally complement the loss of the prokaryotic protein foldase, disulfide oxidase (DsbA), as demonstrated by the reconstitution of periplasmic alkaline phosphatase in Escherichia coli. CONCLUSION The results indicate that PDI8 is a type I transmembrane protein with its catalytic domain facing the lumen of the ER and functions in the oxidation of cysteines to produce disulfide bonds. It likely plays a role in folding newly-synthesized secretory proteins as they translocate across the ER membrane into the lumen. These foundational results open the door to identifying the substrates of PDI8 to enable a more thorough understanding of its function in plants.
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Affiliation(s)
- Christen Y. L. Yuen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Rd., Ag. Science Rm 218, Honolulu, HI 96822 USA
| | - Roger Shek
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Rd., Ag. Science Rm 218, Honolulu, HI 96822 USA
| | - Byung-Ho Kang
- The Chinese University of Hong Kong, School of Life Sciences, Shatin, Hong Kong, SAR China
| | - Kristie Matsumoto
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Rd., Ag. Science Rm 218, Honolulu, HI 96822 USA
| | - Eun Ju Cho
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Rd., Ag. Science Rm 218, Honolulu, HI 96822 USA
| | - David A. Christopher
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Rd., Ag. Science Rm 218, Honolulu, HI 96822 USA
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231
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Xu L, Wang J, Lei M, Li L, Fu Y, Wang Z, Ao M, Li Z. Transcriptome Analysis of Storage Roots and Fibrous Roots of the Traditional Medicinal Herb Callerya speciosa (Champ.) ScHot. PLoS One 2016; 11:e0160338. [PMID: 27486800 PMCID: PMC4972434 DOI: 10.1371/journal.pone.0160338] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/18/2016] [Indexed: 11/22/2022] Open
Abstract
Callerya speciosa (Champ.) ScHot is a woody perennial plant in Fabaceae, the roots of which are used medicinally. The storage roots of C. speciosa are derived from fibrous roots, but not all fibrous roots can develop into storage roots. To detect key genes involved in storage roots formation, we performed Illumina sequencing of the C. speciosa storage roots and fibrous roots. De novo assembly resulted in 161,926 unigenes, which were subsequently annotated by BLAST, GO and KEGG analyses. After expression profiling, 4538 differentially expressed genes were identified. The KEGG pathway enrichment analysis revealed changes in the biosynthesis of cytokinin, phenylpropanoid, starch, sucrose, flavone and other secondary metabolites. Transcription factor-related differentially expressed genes (DEGs) were also identified, including such gene families as GRAS, COL, MIKC, ERF, LBD, and NAC. The DEGs related to light signaling, starch, sugar, photohormones and cell wall-loosening might be involved in the formation of storage roots. This study provides the first transcriptome profiling of C. speciosa roots, data that will facilitate future research of root development and metabolites with medicinal value as well as the breeding of C. speciosa.
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Affiliation(s)
- Li Xu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Jiabin Wang
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Ming Lei
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Li Li
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Yunliu Fu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Zhunian Wang
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Mengfei Ao
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Zhiying Li
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
- * E-mail:
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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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233
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Frank MH, Chitwood DH. Plant chimeras: The good, the bad, and the 'Bizzaria'. Dev Biol 2016; 419:41-53. [PMID: 27381079 DOI: 10.1016/j.ydbio.2016.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/25/2016] [Accepted: 07/01/2016] [Indexed: 01/10/2023]
Abstract
Chimeras - organisms that are composed of cells of more than one genotype - captured the human imagination long before they were formally described and used in the laboratory. These organisms owe their namesake to a fire-breathing monster from Greek mythology that has the head of a lion, the body of a goat, and the tail of a serpent. The first description of a non-fictional chimera dates back to the middle of the seventeenth century when the Florentine gardener Pietro Nati discovered an adventitious shoot growing from the graft junction between sour orange (Citrus aurantium) and citron (Citrus medica). This perplexing chimera that grows with sectors phenotypically resembling each of the citrus progenitors inspired discussion and wonder from the scientific community and was fittingly named the 'Bizzaria'. Initially, the 'Bizzaria' was believed to be an asexual hybrid that formed from a cellular fusion between the grafted parents; however, in-depth cellular analyses carried out centuries later demonstrated that the 'Bizzaria', along with other chimeras, owe their unique sectored appearance to a conglomeration of cells from the two donors. Since this pivotal discovery at the turn of the twentieth century, chimeras have served both as tools and as unique biological phenomena that have contributed to our understanding of plant development at the cellular, tissue, and organismal level. Rapid advancements in genome sequencing technologies have enabled the establishment of new model species with novel morphological and developmental features that enable the generation of chimeric organisms. In this review, we show that genetic mosaic and chimera studies provide a technologically simple way to delve into the organismal, genetic, and genomic inner workings underlying the development of diverse model organisms. Moreover, we discuss the unique opportunity that chimeras present to explore universal principles governing intercellular communication and the coordination of organismal biology in a heterogenomic landscape.
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Affiliation(s)
- Margaret H Frank
- Donald Danforth Plant Science Center, 975 North Warson Rd, Saint Louis, MO 63132, United States.
| | - Daniel H Chitwood
- Donald Danforth Plant Science Center, 975 North Warson Rd, Saint Louis, MO 63132, United States
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234
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Arabidopsis COP1-interacting protein 1 is a positive regulator of ABA response. Biochem Biophys Res Commun 2016; 477:847-853. [PMID: 27372427 DOI: 10.1016/j.bbrc.2016.06.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 11/24/2022]
Abstract
COP1-interacting protein 1 (CIP1, At5g41790) was the first reported interacting protein for CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) of Arabidopsis; however its physiological function has remained unknown for two decades. Here we show that CIP1 is a positive regulator of abscisic acid (ABA) response. CIP1 is mainly expressed in the photosynthetic cells and the vascular tissue, and its promoter activity can be induced by osmotic stress and ABA. The CIP1 protein is localized to the plasma membrane. A T-DNA insertion mutant cip1-1 was then characterized. The mutant is sensitive to osmotic stress and has ABA insensitive phenotypes. RNA sequencing showed that cip1-1 has lower levels of gene expression in abiotic stress response compared with the wild-type. Meanwhile, transcript levels of ABA biosynthesis genes are higher in cip1-1 than in the wild-type. These results suggested that CIP1 is positively involved in ABA response.
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235
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Matthys C, Walton A, Struk S, Stes E, Boyer FD, Gevaert K, Goormachtig S. The Whats, the Wheres and the Hows of strigolactone action in the roots. PLANTA 2016; 243:1327-37. [PMID: 26895337 DOI: 10.1007/s00425-016-2483-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/29/2016] [Indexed: 05/07/2023]
Abstract
Strigolactones control various aspects of plant development, including root architecture. Here, we review how strigolactones act in the root and survey the strigolactone specificity of signaling components that affect root development. Strigolactones are a group of secondary metabolites produced in plants that have been assigned multiple roles, of which the most recent is hormonal activity. Over the last decade, these compounds have been shown to regulate various aspects of plant development, such as shoot branching and leaf senescence, but a growing body of literature suggests that these hormones play an equally important role in the root. In this review, we present all known root phenotypes linked to strigolactones. We examine the expression and presence of the main players in biosynthesis and signaling of these hormones and bring together the available information that allows us to explain how strigolactones act to modulate the root system architecture.
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Affiliation(s)
- Cedrick Matthys
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Sylwia Struk
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - François-Didier Boyer
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique-AgroParisTech, 78026, Versailles Cedex, France
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, Unité Propre de Recherche 2301, Centre National de la Recherche Scientifique, 91198, Gif-Sur-Yvette, France
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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236
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Warschefsky EJ, Klein LL, Frank MH, Chitwood DH, Londo JP, von Wettberg EJB, Miller AJ. Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes. TRENDS IN PLANT SCIENCE 2016; 21:418-437. [PMID: 26698413 DOI: 10.1016/j.tplants.2015.11.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/16/2015] [Accepted: 11/11/2015] [Indexed: 05/18/2023]
Abstract
Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.
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Affiliation(s)
- Emily J Warschefsky
- Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA; Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA
| | - Laura L Klein
- Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132-2918, USA
| | - Daniel H Chitwood
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132-2918, USA
| | - Jason P Londo
- United States Department of Agriculture, Agriculture Research Service: Grape Genetics Research Unit, 630 West North Street, Geneva, NY 14456-1371, USA
| | - Eric J B von Wettberg
- Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA; Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA; Florida International University, International Center for Tropical Botany, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA
| | - Allison J Miller
- Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA.
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237
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Yoshida S, Cui S, Ichihashi Y, Shirasu K. The Haustorium, a Specialized Invasive Organ in Parasitic Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:643-67. [PMID: 27128469 DOI: 10.1146/annurev-arplant-043015-111702] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae.
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Affiliation(s)
- Satoko Yoshida
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
| | - Songkui Cui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
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238
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Affiliation(s)
- Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam/Golm 14476, Germany
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Potsdam/Golm 14476, Germany
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239
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Zhang Z, Zheng Y, Ham BK, Chen J, Yoshida A, Kochian LV, Fei Z, Lucas WJ. Vascular-mediated signalling involved in early phosphate stress response in plants. NATURE PLANTS 2016; 2:16033. [PMID: 27249565 DOI: 10.1038/nplants.2016.33] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/13/2016] [Indexed: 05/09/2023]
Abstract
Depletion of finite global rock phosphate (Pi) reserves will impose major limitations on future agricultural productivity and food security. Hence, modern breeding programmes seek to develop Pi-efficient crops with sustainable yields under reduced Pi fertilizer inputs. In this regard, although the long-term responses of plants to Pi stress are well documented, the early signalling events have yet to be elucidated. Here, we show plant tissue-specific responses to early Pi stress at the transcription level and a predominant role of the plant vascular system in this process. Specifically, imposition of Pi stress induces rapid and major changes in the mRNA population in the phloem translocation stream, and grafting studies have revealed that many hundreds of phloem-mobile mRNAs are delivered to specific sink tissues. We propose that the shoot vascular system acts as the site of root-derived Pi stress perception, and the phloem serves to deliver a cascade of signals to various sinks, presumably to coordinate whole-plant Pi homeostasis.
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Affiliation(s)
- Zhaoliang Zhang
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
| | - Jieyu Chen
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
| | - Akiko Yoshida
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Leon V Kochian
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
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240
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Abstract
Intracellular trafficking and asymmetric localization of RNA molecules within cells are a prevalent process across phyla involved in developmental control and signaling and thus in the determination of cell fate. In addition to intracellular localization, plants support the trafficking of RNA molecules also between cells through plasmodesmata (PD), which has important roles in the cell-to-cell and systemic communication during plant growth and development. Viruses have developed strategies to exploit the underlying plant RNA transport mechanisms for the cell-to-cell and systemic dissemination of infection. In vivo RNA visualization methods have revolutionized the study of RNA dynamics in living cells. However, their application in plants is still in its infancy. To gain insights into the RNA transport mechanisms in plants, we study the localization and transport of Tobacco mosaic virus RNA using MS2 tagging. This technique involves the tagging of the RNA of interest with repeats of an RNA stem-loop (SL) that is derived from the origin of assembly of the bacteriophage MS2 and recruits the MS2 coat protein (MCP). Thus, expression of MCP fused to a fluorescent marker allows the specific visualization of the SL-carrying RNA. Here we describe a detailed protocol for Agrobacterium tumefaciens-mediated transient expression and in vivo visualization of MS2-tagged mRNAs in Nicotiana benthamiana leaves.
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Affiliation(s)
- E J Peña
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata CONICET, Fac. Cs. Exactas, U.N.L.P., La Plata, Argentina
| | - M Heinlein
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France.
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241
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Shabala S, White RG, Djordjevic MA, Ruan YL, Mathesius U. Root-to-shoot signalling: integration of diverse molecules, pathways and functions. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:87-104. [PMID: 32480444 DOI: 10.1071/fp15252] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/06/2015] [Indexed: 05/23/2023]
Abstract
Plant adaptive potential is critically dependent upon efficient communication and co-ordination of resource allocation and signalling between above- and below-ground plant parts. Plant roots act as gatekeepers that sense and encode information about soil physical, chemical and biological factors, converting them into a sophisticated network of signals propagated both within the root itself, and also between the root and shoot, to optimise plant performance for a specific set of conditions. In return, plant roots receive and decode reciprocal information coming from the shoot. The communication modes are highly diverse and include a broad range of physical (electric and hydraulic signals, propagating Ca2+ and ROS waves), chemical (assimilates, hormones, peptides and nutrients), and molecular (proteins and RNA) signals. Further, different signalling systems operate at very different timescales. It remains unclear whether some of these signalling systems operate in a priming mode(s), whereas others deliver more specific information about the nature of the signal, or whether they carry the same 'weight'. This review summarises the current knowledge of the above signalling mechanisms, and reveals their hierarchy, and highlights the importance of integration of these signalling components, to enable optimal plant functioning in a dynamic environment.
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Affiliation(s)
- Sergey Shabala
- School of Land and Food, University of Tasmania, Private Bag 54, Hobart, Tas. 7001, Australia
| | | | - Michael A Djordjevic
- Plant Science Division, Research School of Biology, Building 134, Linnaeus Way, The Australian National University, Canberra, ACT 2601, Australia
| | - Yong-Ling Ruan
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Ulrike Mathesius
- Plant Science Division, Research School of Biology, Building 134, Linnaeus Way, The Australian National University, Canberra, ACT 2601, Australia
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242
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Bilichak A, Kovalchuk I. Transgenerational response to stress in plants and its application for breeding. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2081-92. [PMID: 26944635 DOI: 10.1093/jxb/erw066] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A growing number of reports indicate that plants possess the ability to maintain a memory of stress exposure throughout their ontogenesis and even transmit it faithfully to the following generation. Some of the features of transgenerational memory include elevated genome instability, a higher tolerance to stress experienced by parents, and a cross-tolerance. Although the underlying molecular mechanisms of this phenomenon are not clear, a likely contributing factor is the absence of full-scale reprogramming of the epigenetic landscape during gametogenesis; therefore, epigenetic marks can occasionally escape the reprogramming process and can be passed on to the progeny. To date, it is not entirely clear which part of the epigenetic landscape is more likely to escape the reprogramming events, and whether such a process is random or directed and sequence specific. The identification of specific epigenetic marks associated with specific stressors would allow generation of stress-tolerant plants through the recently discovered techniques for precision epigenome engineering. The engineered DNA-binding domains (e.g. ZF, TALE, and dCas9) fused to particular chromatin modifiers would make it possible to target epigenetic modifications to the selected loci, probably allowing stress tolerance to be achieved in the progeny. This approach, termed epigenetic breeding, along with other methods has great potential to be used for both the assessment of the propagation of epigenetic marks across generations and trait improvement in plants. In this communication, we provide a short overview of recent reports demonstrating a transgenerational response to stress in plants, and discuss the underlying potential molecular mechanisms of this phenomenon and its use for plant biotechnology applications.
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Affiliation(s)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, AB, T1K 3M4, Canada
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243
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Toscano-Morales R, Xoconostle-Cázares B, Martínez-Navarro AC, Ruiz-Medrano R. AtTCTP2 mRNA and protein movement correlates with formation of adventitious roots in tobacco. PLANT SIGNALING & BEHAVIOR 2016; 11:e1071003. [PMID: 26237533 PMCID: PMC4883931 DOI: 10.1080/15592324.2015.1071003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/01/2015] [Accepted: 07/04/2015] [Indexed: 05/11/2023]
Abstract
The Translationally Controlled Tumor Proteins, or TCTP, is a superfamily of exclusively eukaryotic proteins essential in the regulation of proliferation and general growth. However, it is clear that these are multifunctional proteins given (1) the pleiotropic effects of its mutations, and (2), the multiple processes in which this protein is involved. TCTP function in general is conserved, since Arabidopsis AtTCTP1 can rescue a Drosophila mutant, and vice versa. It has become clear, however, that these proteins may have "taxon-specific" functions. In the case of plants, mRNA and/or proteins have been found in the phloem translocation stream of different species, suggesting a role in long-distance signaling. We have found that a second Arabidopsis TCTP gene, AtTCTP2, codes for a protein that moves long-distance through a graft union in tobacco. Interestingly, the mRNA is also transported long-distance. Both mRNA and protein move long-distance; interestingly, the movement, while more efficient from source to sink tissues, also occurs in the opposite direction. The protein reaches the nuclei of parenchyma cells and adventitious roots. Furthermore, it is clear that the long-distance delivery of AtTCTP2 protein and mRNA is required for the induction of adventitious roots. A model is presented that accounts for these observations.
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Affiliation(s)
| | | | | | - Roberto Ruiz-Medrano
- Department of Biotechnology and Bioengineering; CINVESTAV; Zacatenco, Mexico DF, Mexico
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244
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Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L. A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence. FRONTIERS IN PLANT SCIENCE 2016; 7:983. [PMID: 27462324 PMCID: PMC4940393 DOI: 10.3389/fpls.2016.00983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/21/2016] [Indexed: 05/05/2023]
Abstract
Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; conversely, in a saqr T-DNA knockout (KO) line, starch accumulation is increased. Meta-analysis of public microarray data indicates that SAQR expression is correlated with expression of a subset of genes involved in senescence, defense, and stress responses. SAQR promoter::GUS expression analysis reveals that SAQR expression increases after leaf expansion and photosynthetic capacity have peaked, just prior to visible natural senescence. SAQR is expressed predominantly within leaf and cotyledon vasculature, increasing in intensity as natural senescence continues, and then decreasing prior to death. In contrast, under experimentally induced senescence, SAQR expression increases in vasculature of cotyledons but not in true leaves. In SAQR KO line, the transcript level of the dirigent-like disease resistance gene (AT1G22900) is increased, while that of the Early Light Induced Protein 1 gene (ELIP1, AT3G22840) is decreased. Taken together, these data indicate that SAQR may function in the QQS network, playing a role in integration of primary metabolism with adaptation to internal and environmental changes, specifically those that affect the process of senescence.
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Affiliation(s)
- Dallas C. Jones
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Sheng Huang
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Chuanlong Du
- Department of Statistics, Iowa State University, AmesIA, USA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, AmesIA, USA
| | - Ragothaman M. Yennamalli
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agriculture Research Service, AmesIA, USA
| | - Taner Z. Sen
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agriculture Research Service, AmesIA, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, AmesIA, USA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
| | - Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
- *Correspondence: Ling Li,
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245
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Igarashi M, Hatsuyama Y, Harada T, Fukasawa-Akada T. Biotechnology and apple breeding in Japan. BREEDING SCIENCE 2016; 66:18-33. [PMID: 27069388 PMCID: PMC4780799 DOI: 10.1270/jsbbs.66.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/23/2015] [Indexed: 05/11/2023]
Abstract
Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.
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Affiliation(s)
- Megumi Igarashi
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
| | - Yoshimichi Hatsuyama
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center,
Fukutami 24, Botandaira, Kuroishi, Aomori 036-0332,
Japan
| | - Takeo Harada
- Department of Agriculture and Life Science, Hirosaki University,
Bunkyouchou 3, Hirosaki, Aomori 036-8563,
Japan
| | - Tomoko Fukasawa-Akada
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
- Corresponding author (e-mail: )
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246
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Saplaoura E, Kragler F. Mobile Transcripts and Intercellular Communication in Plants. DEVELOPMENTAL SIGNALING IN PLANTS 2016; 40:1-29. [DOI: 10.1016/bs.enz.2016.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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247
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Shah JN, Kirioukhova O, Pawar P, Tayyab M, Mateo JL, Johnston AJ. Depletion of Key Meiotic Genes and Transcriptome-Wide Abiotic Stress Reprogramming Mark Early Preparatory Events Ahead of Apomeiotic Transition. FRONTIERS IN PLANT SCIENCE 2016; 7:1539. [PMID: 27833618 PMCID: PMC5080521 DOI: 10.3389/fpls.2016.01539] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/30/2016] [Indexed: 05/19/2023]
Abstract
Molecular dissection of apomixis - an asexual reproductive mode - is anticipated to solve the enigma of loss of meiotic sex, and to help fixing elite agronomic traits. The Brassicaceae genus Boechera comprises of both sexual and apomictic species, permitting comparative analyses of meiotic circumvention (apomeiosis) and parthenogenesis. Whereas previous studies reported local transcriptome changes during these events, it remained unclear whether global changes associated with hybridization, polyploidy and environmental adaptation that arose during evolution of Boechera might serve as (epi)genetic regulators of early development prior apomictic initiation. To identify these signatures during vegetative stages, we compared seedling RNA-seq transcriptomes of an obligate triploid apomict and a diploid sexual, both isolated from a drought-prone habitat. Uncovered were several genes differentially expressed between sexual and apomictic seedlings, including homologs of meiotic genes ASYNAPTIC 1 (ASY1) and MULTIPOLAR SPINDLE 1 (MPS1) that were down-regulated in apomicts. An intriguing class of apomict-specific deregulated genes included several NAC transcription factors, homologs of which are known to be transcriptionally reprogrammed during abiotic stress in other plants. Deregulation of both meiotic and stress-response genes during seedling stages might possibly be important in preparation for meiotic circumvention, as similar transcriptional alteration was discernible in apomeiotic floral buds too. Furthermore, we noted that the apomict showed better tolerance to osmotic stress in vitro than the sexual, in conjunction with significant upregulation of a subset of NAC genes. In support of the current model that DNA methylation epigenetically regulates stress, ploidy, hybridization and apomixis, we noted that ASY1, MPS1 and NAC019 homologs were deregulated in Boechera seedlings upon DNA demethylation, and ASY1 in particular seems to be repressed by global DNA methylation exclusively in the apomicts. Variability in stress and transcriptional response in a diploid apomict, which is geographically distinct from the triploid apomict, pinpoints both common and independent features of apomixis evolution. Our study provides a molecular frame-work to investigate how the adaptive traits associated with the evolutionary history of apomicts co-adapted with meiotic gene deregulation at early developmental stage, in order to predate meiotic recombination, which otherwise is thought to be favorable in stress and low-fitness conditions.
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Affiliation(s)
- Jubin N. Shah
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Olga Kirioukhova
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Pallavi Pawar
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Muhammad Tayyab
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Juan L. Mateo
- Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- *Correspondence: Amal J. Johnston, ; Juan L. Mateo,
| | - Amal J. Johnston
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Amal J. Johnston, ; Juan L. Mateo,
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248
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Kopriva S, Calderwood A, Weckopp SC, Koprivova A. Plant sulfur and Big Data. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:1-10. [PMID: 26706053 DOI: 10.1016/j.plantsci.2015.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 05/20/2023]
Abstract
Sulfur is an essential mineral nutrient for plants, therefore, the pathways of its uptake and assimilation have been extensively studied. Great progress has been made in elucidation of the individual genes and enzymes and their regulation. Sulfur assimilation has been intensively investigated by -omics technologies and has been target of several genome wide genetic approaches. This brought a significant step in our understanding of the regulation of the pathway and its integration in cellular metabolism. However, the large amount of information derived from other experiments not directly targeting sulfur has also brought new and exciting insights into processes affecting sulfur homeostasis. In this review we will integrate the findings of the targeted experiments with those that brought unintentional progress in sulfur research, and will discuss how to synthesize the large amount of information available in various repositories into a meaningful dissection of the regulation of a specific metabolic pathway. We then speculate how this might be used to further advance knowledge on control of sulfur metabolism and what are the main questions to be answered.
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Affiliation(s)
- Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | | | - Silke C Weckopp
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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249
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Bleckmann A, Dresselhaus T. Fluorescent whole-mount RNA in situ hybridization (F-WISH) in plant germ cells and the fertilized ovule. Methods 2015; 98:66-73. [PMID: 26521978 DOI: 10.1016/j.ymeth.2015.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 12/17/2022] Open
Abstract
First evidence on gene function and regulation is provided by the cellular expression pattern in complex tissues. However, to understand the activity of a specific gene, it is essential to analyze the regulatory network, which controls the spatio-temporal translation pattern during the entire life span of the transcribed mRNA. To explore mechanisms which control mRNA abundance and localization in space and time, it is necessary to visualize mRNAs quantitatively with a subcellular resolution, without sectioning the tissues. We have adapted and optimized a protocol for colorimetric whole-mount RNA in situ hybridization (WISH) using egg cell-specific digoxigenin (DIG) labeled probes (Hejátko et al., 2006) [1] on ovules and early seeds of Arabidopsis. Furthermore, we established a fluorescent whole-mount RNA in situ hybridization (F-WISH) protocol, which allows mRNA visualization on a subcellular level. The polar localized mRNA of SBT4.13, encoding a subtilase, was identified using this protocol. Both methods are described and discussed in detail. Additionally a (F)-WISH flow-chart is provided along with a troubleshooting table.
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Affiliation(s)
- Andrea Bleckmann
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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250
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Toscano-Morales R, Xoconostle-Cázares B, Cabrera-Ponce JL, Hinojosa-Moya J, Ruiz-Salas JL, Galván-Gordillo SV, Guevara-González RG, Ruiz-Medrano R. AtTCTP2, an Arabidopsis thaliana homolog of Translationally Controlled Tumor Protein, enhances in vitro plant regeneration. FRONTIERS IN PLANT SCIENCE 2015; 6:468. [PMID: 26191065 PMCID: PMC4489097 DOI: 10.3389/fpls.2015.00468] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 06/12/2015] [Indexed: 05/20/2023]
Abstract
The Translationally Controlled Tumor Protein (TCTP) is a central regulator of cell proliferation and differentiation in animals, and probably also in plants. Arabidopsis harbors two TCTP genes, AtTCTP1 (At3g16640), which is an important mitotic regulator, and AtTCTP2 (At3g05540), which is considered a pseudogene. Nevertheless, we have obtained evidence suggesting that this gene is functional. Indeed, a T-DNA insertion mutant, SALK_045146, displays a lethal phenotype during early rosette stage. Also, both the AtTCTP2 promoter and structural gene are functional, and heterozygous plants show delayed development. AtTCTP1 cannot compensate for the loss of AtTCTP2, since the accumulation levels of the AtTCTP1 transcript are even higher in heterozygous plants than in wild-type plants. Leaf explants transformed with Agrobacterium rhizogenes harboring AtTCTP2, but not AtTCTP1, led to whole plant regeneration with a high frequency. Insertion of a sequence present in AtTCTP1 but absent in AtTCTP2 demonstrates that it suppresses the capacity for plant regeneration; also, this phenomenon is enhanced by the presence of TCTP (AtTCTP1 or 2) in the nuclei of root cells. This confirms that AtTCTP2 is not a pseudogene and suggests the involvement of certain TCTP isoforms in vegetative reproduction in some plant species.
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Affiliation(s)
- Roberto Toscano-Morales
- Laboratory of Plant Molecular Biology, Department of Biotechnology and Bioengineering, CINVESTAVMexico City, Mexico
| | - Beatriz Xoconostle-Cázares
- Laboratory of Plant Molecular Biology, Department of Biotechnology and Bioengineering, CINVESTAVMexico City, Mexico
| | | | - Jesús Hinojosa-Moya
- Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, Ciudad UniversitariaPuebla, Mexico
| | - Jorge L. Ruiz-Salas
- Laboratory of Plant Molecular Biology, Department of Biotechnology and Bioengineering, CINVESTAVMexico City, Mexico
| | - Santiago V. Galván-Gordillo
- Laboratory of Plant Molecular Biology, Department of Biotechnology and Bioengineering, CINVESTAVMexico City, Mexico
| | - Ramón G. Guevara-González
- CA Ingenieria de Biosistemas, Centro Universitario Cerro de las Campanas, Universidad Autónoma de QuerétaroSantiago de Querétaro, Mexico
| | - Roberto Ruiz-Medrano
- Laboratory of Plant Molecular Biology, Department of Biotechnology and Bioengineering, CINVESTAVMexico City, Mexico
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