1
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Jo L, Kajala K. ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images. J Exp Bot 2024:erae043. [PMID: 38329371 DOI: 10.1093/jxb/erae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Indexed: 02/09/2024]
Abstract
As plant research generates an ever-growing volume of spatial quantitative data, the need for decentralized and user-friendly visualization tools to explore large and complex datasets tools becomes crucial. Existing resources, such as the Plant eFP (electronic Fluorescent Pictograph) viewer, have played a pivotal role on the communication of gene expression data across many plant species. However, although widely used by the plant research community, the Plant eFP viewer lacks open and user-friendly tools for the creation of customized expression maps independently. Plant biologists with less coding experience can often encounter challenges when attempting to explore ways to communicate their own spatial quantitative data. We present 'ggPlantmap' an open-source R package designed to address this challenge by providing an easy and user-friendly method for the creation of ggplot representative maps from plant images. ggPlantmap is built in R, one of the most used languages in biology to empower plant scientists to create and customize eFP-like viewers tailored to their experimental data. Here, we provide an overview of the package and tutorials that are accessible even to users with minimal R programming experience. We hope that ggPlantmap can assist the plant science community, fostering innovation and improving our understanding of plant development and function.
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Affiliation(s)
- Leonardo Jo
- Experimental and Computational Plant Development, Institute of Environment Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Kaisa Kajala
- Experimental and Computational Plant Development, Institute of Environment Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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2
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Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, Nirmal N, Suresh K, Ursache R, Mason GA, Gouran M, West DA, Borowsky AT, Shackel KA, Sinha N, Bailey-Serres J, Geldner N, Li S, Franke RB, Brady SM. A suberized exodermis is required for tomato drought tolerance. Nat Plants 2024; 10:118-130. [PMID: 38168610 PMCID: PMC10808073 DOI: 10.1038/s41477-023-01567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/23/2023] [Indexed: 01/05/2024]
Abstract
Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Lidor Shaar-Moshe
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Concepción Manzano
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Prakash Timilsena
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Damien De Bellis
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Sharon Gray
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Julia Holbein
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - He Yang
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Sana Mohammad
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Niba Nirmal
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Kiran Suresh
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Robertas Ursache
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Mona Gouran
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Kenneth A Shackel
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Niko Geldner
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Rochus Benni Franke
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.
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3
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Pantazopoulou CK, Buti S, Nguyen CT, Oskam L, Weits DA, Farmer EE, Kajala K, Pierik R. Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics. Nat Commun 2023; 14:5827. [PMID: 37730832 PMCID: PMC10511701 DOI: 10.1038/s41467-023-41530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca2+]cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes reduce touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.
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Affiliation(s)
- Chrysoula K Pantazopoulou
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands.
| | - Sara Buti
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Chi Tam Nguyen
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Lisa Oskam
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Daan A Weits
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Kaisa Kajala
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands.
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
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4
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Caspi Y, Pantazopoulou CK, Prompers JJ, Pieterse CMJ, Hulshoff Pol H, Kajala K. Why did glutamate, GABA, and melatonin become intercellular signalling molecules in plants? eLife 2023; 12:e83361. [PMID: 37338964 DOI: 10.7554/elife.83361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/14/2023] [Indexed: 06/21/2023] Open
Abstract
Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, γ-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.
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Affiliation(s)
- Yaron Caspi
- Institute of Environmental Biology, Department of Biology, Utrecht University, Utrecht, Netherlands
- Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Jeanine J Prompers
- Department of Radiology, Imaging Division, University Medical Center Utrecht, Utrecht, Netherlands
| | - Corné M J Pieterse
- Institute of Environmental Biology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Kaisa Kajala
- Institute of Environmental Biology, Department of Biology, Utrecht University, Utrecht, Netherlands
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5
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Courbier S, Snoek BL, Kajala K, Li L, van Wees SCM, Pierik R. Mechanisms of far-red light-mediated dampening of defense against Botrytis cinerea in tomato leaves. Plant Physiol 2021; 187:1250-1266. [PMID: 34618050 PMCID: PMC8566310 DOI: 10.1093/plphys/kiab354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense tradeoff. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato (Solanum lycopersicum) plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-h time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affected plant immune responses under the WL+FR condition. This study improves our understanding of the growth-immunity tradeoff, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems.
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Affiliation(s)
- Sarah Courbier
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, The Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Linge Li
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
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6
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Artur MAS, Kajala K. Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments. Plant Cell Environ 2021; 44:3211-3222. [PMID: 34196969 PMCID: PMC8518057 DOI: 10.1111/pce.14143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/25/2021] [Indexed: 05/21/2023]
Abstract
Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho-physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co-option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review, we address how the study of CCMs and DT has provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co-option, conservation and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.
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Affiliation(s)
- Mariana A. S. Artur
- Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
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7
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Kajala K, Gouran M, Shaar-Moshe L, Mason GA, Rodriguez-Medina J, Kawa D, Pauluzzi G, Reynoso M, Canto-Pastor A, Manzano C, Lau V, Artur MAS, West DA, Gray SB, Borowsky AT, Moore BP, Yao AI, Morimoto KW, Bajic M, Formentin E, Nirmal NA, Rodriguez A, Pasha A, Deal RB, Kliebenstein DJ, Hvidsten TR, Provart NJ, Sinha NR, Runcie DE, Bailey-Serres J, Brady SM. Innovation, conservation, and repurposing of gene function in root cell type development. Cell 2021; 184:5070. [PMID: 34534466 DOI: 10.1016/j.cell.2021.08.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Courbier S, Grevink S, Sluijs E, Bonhomme PO, Kajala K, Van Wees SCM, Pierik R. Far-red light promotes Botrytis cinerea disease development in tomato leaves via jasmonate-dependent modulation of soluble sugars. Plant Cell Environ 2020; 43:2769-2781. [PMID: 32833234 DOI: 10.1101/2020.05.25.114439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 05/27/2023]
Abstract
Plants experience a decrease in the red:far-red light ratio (R:FR) when grown at high planting density. In addition to eliciting the shade avoidance response, low R:FR also enhances plant susceptibility to pathogens via modulation of defense hormone-mediated responses. However, other mechanisms, also affected by low R:FR, have not been considered as potential components in FR-induced susceptibility. Here, we identify FR-induced accumulation of leaf soluble sugars as a novel component of FR-induced susceptibility. We observed that phytochrome inactivation by FR or phytochrome B mutation was associated with elevated leaf glucose and fructose levels and enhanced disease severity caused by Botrytis cinerea. By experimentally manipulating internal leaf sugar levels, we found that the FR-induced susceptibility in tomato was partly sugar-dependent. Further analysis revealed that the observed sugar accumulation in supplemental FR occurred in a jasmonic acid (JA)-dependent manner, and the JA biosynthesis mutant def1 also displayed elevated soluble sugar levels, which was rescued by exogenous methyl jasmonate (MeJA) application. We propose that the reduced JA responsiveness under low R:FR promotes disease symptoms not only via dampened induction of defense responses, but also via increased levels of soluble sugars that supports pathogen growth in tomato leaves.
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Affiliation(s)
- Sarah Courbier
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Sanne Grevink
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Emma Sluijs
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Pierre-Olivier Bonhomme
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
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9
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Courbier S, Grevink S, Sluijs E, Bonhomme P, Kajala K, Van Wees SCM, Pierik R. Far-red light promotes Botrytis cinerea disease development in tomato leaves via jasmonate-dependent modulation of soluble sugars. Plant Cell Environ 2020; 43:2769-2781. [PMID: 32833234 PMCID: PMC7693051 DOI: 10.1111/pce.13870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 05/12/2023]
Abstract
Plants experience a decrease in the red:far-red light ratio (R:FR) when grown at high planting density. In addition to eliciting the shade avoidance response, low R:FR also enhances plant susceptibility to pathogens via modulation of defense hormone-mediated responses. However, other mechanisms, also affected by low R:FR, have not been considered as potential components in FR-induced susceptibility. Here, we identify FR-induced accumulation of leaf soluble sugars as a novel component of FR-induced susceptibility. We observed that phytochrome inactivation by FR or phytochrome B mutation was associated with elevated leaf glucose and fructose levels and enhanced disease severity caused by Botrytis cinerea. By experimentally manipulating internal leaf sugar levels, we found that the FR-induced susceptibility in tomato was partly sugar-dependent. Further analysis revealed that the observed sugar accumulation in supplemental FR occurred in a jasmonic acid (JA)-dependent manner, and the JA biosynthesis mutant def1 also displayed elevated soluble sugar levels, which was rescued by exogenous methyl jasmonate (MeJA) application. We propose that the reduced JA responsiveness under low R:FR promotes disease symptoms not only via dampened induction of defense responses, but also via increased levels of soluble sugars that supports pathogen growth in tomato leaves.
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Affiliation(s)
- Sarah Courbier
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Sanne Grevink
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Emma Sluijs
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Pierre‐Olivier Bonhomme
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Saskia C. M. Van Wees
- Plant‐Microbe Interactions, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
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10
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Bjornson M, Kajala K, Zipfel C, Ding P. Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue. Bio Protoc 2020; 10:e3799. [PMID: 33659453 DOI: 10.21769/bioprotoc.3799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/10/2020] [Accepted: 08/22/2020] [Indexed: 12/17/2022] Open
Abstract
Transcriptome analysis can provide clues to biological processes affected in different genetic backgrounds or/and under various conditions. The price of RNA sequencing (RNA-seq) has decreased enough so that medium- to large-scale transcriptome analyses in a range of conditions are feasible. However, the price and variety of options for library preparation of RNA-seq can still be daunting to those who would like to use RNA-seq for their first time or for a single experiment. Among the criteria for selecting a library preparation protocol are the method of RNA isolation, nucleotide fragmentation to obtain desired size range, and library indexing to pool sequencing samples for multiplexing. Here, we present a high-quality and a high-throughput option for preparing libraries from polyadenylated mRNA for transcriptome analysis. Both high-quality and high-throughput protocol options include steps of mRNA enrichment through magnetic bead-enabled precipitation of the poly-A tail, cDNA synthesis, and then fragmentation and adapter addition simultaneously through Tn5-mediated 'tagmentation'. All steps of the protocols have been validated with Arabidopsis thaliana leaf and seedling tissues and streamlined to work together, with minimal cost in money and time, thus intended to provide a beginner-friendly start-to-finish RNA-seq library preparation for transcriptome analysis.
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Affiliation(s)
- Marta Bjornson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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11
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Gray SB, Rodriguez‐Medina J, Rusoff S, Toal TW, Kajala K, Runcie DE, Brady SM. Translational regulation contributes to the elevated CO 2 response in two Solanum species. Plant J 2020; 102:383-397. [PMID: 31797460 PMCID: PMC7216843 DOI: 10.1111/tpj.14632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 05/12/2023]
Abstract
Understanding the impact of elevated CO2 (eCO2 ) in global agriculture is important given climate change projections. Breeding climate-resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2 , from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2 .
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Affiliation(s)
- Sharon B. Gray
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Joel Rodriguez‐Medina
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Samuel Rusoff
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Ted W. Toal
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
- Present address:
Plant EcophysiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Daniel E. Runcie
- Department of Plant SciencesUniversity of California, DavisOne Shields AvenueDavisCA95616USA
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
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12
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Reynoso MA, Kajala K, Bajic M, West DA, Pauluzzi G, Yao AI, Hatch K, Zumstein K, Woodhouse M, Rodriguez-Medina J, Sinha N, Brady SM, Deal RB, Bailey-Serres J. Evolutionary flexibility in flooding response circuitry in angiosperms. Science 2019; 365:1291-1295. [PMID: 31604238 PMCID: PMC7710369 DOI: 10.1126/science.aax8862] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/26/2019] [Indexed: 11/02/2022]
Abstract
Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergence-activated genes with signatures of overlapping cis regulation by four transcription factor families. Syntenic genes are more highly expressed than nonsyntenic genes, yet both can have the cis motifs and chromatin accessibility associated with submergence up-regulation. Whereas the flexible circuitry spans the eudicot-monocot divide, the frequency of specific cis motifs, extent of chromatin accessibility, and degree of submergence activation are more prevalent in the wetland crop and may have adaptive importance.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, CA, USA
| | - Kaisa Kajala
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA , USA
- Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, GA, USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA, USA
| | - Donnelly A West
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, CA, USA
| | - Andrew I Yao
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA , USA
| | - Kathryn Hatch
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Kristina Zumstein
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA
| | - Margaret Woodhouse
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA
| | - Joel Rodriguez-Medina
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA , USA
| | - Neelima Sinha
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA.
| | - Siobhan M Brady
- Department of Plant Biology, Division of Biological Sciences, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA , USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA, USA.
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, CA, USA.
- Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, Netherlands
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13
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Kajala K, Walker KL, Mitchell GS, Krämer U, Cherry SR, Brady SM. Real-time whole-plant dynamics of heavy metal transport in Arabidopsis halleri and Arabidopsis thaliana by gamma-ray imaging. Plant Direct 2019; 3:e00131. [PMID: 31309170 PMCID: PMC6589544 DOI: 10.1002/pld3.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/30/2019] [Accepted: 03/08/2019] [Indexed: 06/08/2023]
Abstract
Heavy metals such as zinc are essential for plant growth, but toxic at high concentrations. Despite our knowledge of the molecular mechanisms of heavy metal uptake by plants, experimentally addressing the real-time whole-plant dynamics of heavy metal uptake and partitioning has remained a challenge. To overcome this, we applied a high sensitivity gamma-ray imaging system to image uptake and transport of radioactive 65Zn in whole-plant assays of Arabidopsis thaliana and the Zn hyperaccumulator Arabidopsis halleri. We show that our system can be used to quantitatively image and measure uptake and root-to-shoot translocation dynamics of zinc in real time. In the metal hyperaccumulator Arabidopsis halleri, 65Zn uptake and transport from its growth media to the shoot occurs rapidly and on time scales similar to those reported in rice. In transgenic A. halleri plants in which expression of the zinc transporter gene HMA4 is suppressed by RNAi, 65Zn uptake is completely abolished.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Biology and Genome CenterUniversity of California DavisDavisCalifornia
- Plant EcophysiologyInstitute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Katherine L. Walker
- Department of Biomedical EngineeringUniversity of California DavisDavisCalifornia
| | - Gregory S. Mitchell
- Department of Biomedical EngineeringUniversity of California DavisDavisCalifornia
| | - Ute Krämer
- Molecular Genetics and Physiology of PlantsRuhr University BochumBochumGermany
| | - Simon R. Cherry
- Department of Biomedical EngineeringUniversity of California DavisDavisCalifornia
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUniversity of California DavisDavisCalifornia
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14
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Reynoso MA, Pauluzzi GC, Cabanlit S, Velasco J, Bazin J, Deal R, Brady S, Sinha N, Bailey-Serres J, Kajala K. Isolation of Nuclei in Tagged Cell Types (INTACT), RNA Extraction and Ribosomal RNA Degradation to Prepare Material for RNA-Seq. Bio Protoc 2018; 8:e2458. [PMID: 34286007 DOI: 10.21769/bioprotoc.2458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/02/2022] Open
Abstract
Gene expression is dynamically regulated on many levels, including chromatin accessibility and transcription. In order to study these nuclear regulatory events, we describe our method to purify nuclei with Isolation of Nuclei in TAgged Cell Types (INTACT). As nuclear RNA is low in polyadenylated transcripts and conventional pulldown methods would not capture non-polyadenylated pre-mRNA, we also present our method to remove ribosomal RNA from the total nuclear RNA in preparation for nuclear RNA-Seq.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Jérémie Bazin
- IPS2, Institute of Plant Science-Paris Saclay (CNRS-INRA), University of Paris-Saclay, Orsay, France
| | | | - Siobhan Brady
- Department of Plant Biology, UC Davis, Davis, CA, USA.,Genome Center, UC Davis, Davis, CA, USA
| | - Neelima Sinha
- Department of Plant Biology, UC Davis, Davis, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Kaisa Kajala
- Department of Plant Biology, UC Davis, Davis, CA, USA.,Genome Center, UC Davis, Davis, CA, USA
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15
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Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. Plant Cell 2018. [PMID: 29229750 DOI: 10.1101/167932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.
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Affiliation(s)
- Kelsey A Maher
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mauricio Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Margaret Woodhouse
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kerry Bubb
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Michael W Dorrity
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Christine Queitsch
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
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16
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Reynoso MA, Pauluzzi GC, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal R, Sinha NR, Brady SM, Bailey-Serres J. Nuclear Transcriptomes at High Resolution Using Retooled INTACT. Plant Physiol 2018; 176:270-281. [PMID: 28956755 PMCID: PMC5761756 DOI: 10.1104/pp.17.00688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/26/2017] [Indexed: 05/03/2023]
Abstract
Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here, we describe transfer of the isolation of nuclei from tagged specific cell types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear-envelope-targeting domain of the nuclear tagging fusion (NTF) protein with an outer nuclear-envelope-anchored domain. This modified NTF was combined with codon-optimized Escherichia coli BirA in a single T-DNA construct. We also developed inexpensive methods for INTACT, T-DNA insertion mapping, and profiling of the complete nuclear transcriptome, including a ribosomal RNA degradation procedure that minimizes pre-ribosomal RNA (pre-rRNA) transcripts. A high-resolution comparison of nuclear and steady-state poly(A)+ transcript populations of seedling root tips confirmed the capture of pre-messenger RNA (pre-mRNA) and exposed distinctions in diversity and abundance of the nuclear and total transcriptomes. This retooled INTACT can enable high-resolution monitoring of the nuclear transcriptome and chromatin in specific cell types of rice and other species.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Kaisa Kajala
- Department of Plant Biology, University of California, Davis, California 95616
- Genome Center, University of California, Davis, California 95616
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jérémie Bazin
- IPS2, Institute of Plant Science-Paris Saclay (CNRS-INRA), University of Paris-Saclay, F-911405, Orsay, France
| | - Roger Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, California 95616
- Genome Center, University of California, Davis, California 95616
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
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17
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Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. Plant Cell 2018; 30:15-36. [PMID: 29229750 PMCID: PMC5810565 DOI: 10.1105/tpc.17.00581] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/30/2017] [Accepted: 12/06/2017] [Indexed: 05/19/2023]
Abstract
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.
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Affiliation(s)
- Kelsey A Maher
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mauricio Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Margaret Woodhouse
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kerry Bubb
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Michael W Dorrity
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Christine Queitsch
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
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18
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Turco GM, Kajala K, Kunde‐Ramamoorthy G, Ngan C, Olson A, Deshphande S, Tolkunov D, Waring B, Stelpflug S, Klein P, Schmutz J, Kaeppler S, Ware D, Wei C, Etchells JP, Brady SM. DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytol 2017; 214:1213-1229. [PMID: 28186631 PMCID: PMC5655736 DOI: 10.1111/nph.14448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/19/2016] [Indexed: 05/23/2023]
Abstract
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.
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Affiliation(s)
- Gina M. Turco
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | | | - Chew‐Yee Ngan
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory1 Bungtown RoadCold Spring HarborNY11724USA
| | | | - Denis Tolkunov
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Barbara Waring
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | - Scott Stelpflug
- Department of Agronomy and Great Lakes Bioenergy Research CenterUniversity of Wisconsin1575 Linden DriveMadisonWI53706USA
| | - Patricia Klein
- Institute for Plant Genomics and Biotechnology and Department of Horticultural SciencesTexas A and M UniversityCollege StationTX77843USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
- HudsonAlpha Institute for Biotechnology601 Genome Way NWHuntsvilleAL35806USA
| | - Shawn Kaeppler
- Department of Agronomy and Great Lakes Bioenergy Research CenterUniversity of Wisconsin1575 Linden DriveMadisonWI53706USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory1 Bungtown RoadCold Spring HarborNY11724USA
- USDA‐ARSIthacaNY14853USA
| | - Chia‐Lin Wei
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - J. Peter Etchells
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
- School of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH3 1LEUK
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
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19
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Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol 2014; 166:455-69. [PMID: 24868032 PMCID: PMC4213079 DOI: 10.1104/pp.114.239392] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/26/2014] [Indexed: 05/18/2023]
Abstract
Agrobacterium rhizogenes (or Rhizobium rhizogenes) is able to transform plant genomes and induce the production of hairy roots. We describe the use of A. rhizogenes in tomato (Solanum spp.) to rapidly assess gene expression and function. Gene expression of reporters is indistinguishable in plants transformed by Agrobacterium tumefaciens as compared with A. rhizogenes. A root cell type- and tissue-specific promoter resource has been generated for domesticated and wild tomato (Solanum lycopersicum and Solanum pennellii, respectively) using these approaches. Imaging of tomato roots using A. rhizogenes coupled with laser scanning confocal microscopy is facilitated by the use of a membrane-tagged protein fused to a red fluorescent protein marker present in binary vectors. Tomato-optimized isolation of nuclei tagged in specific cell types and translating ribosome affinity purification binary vectors were generated and used to monitor associated messenger RNA abundance or chromatin modification. Finally, transcriptional reporters, translational reporters, and clustered regularly interspaced short palindromic repeats-associated nuclease9 genome editing demonstrate that SHORT-ROOT and SCARECROW gene function is conserved between Arabidopsis (Arabidopsis thaliana) and tomato.
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Affiliation(s)
- Mily Ron
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Kaisa Kajala
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Germain Pauluzzi
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Dongxue Wang
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Mauricio A Reynoso
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Kristina Zumstein
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Jasmine Garcha
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Sonja Winte
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Helen Masson
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Soichi Inagaki
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Fernán Federici
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Neelima Sinha
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Roger B Deal
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Julia Bailey-Serres
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Siobhan M Brady
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
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20
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Kajala K, Ramakrishna P, Fisher A, C. Bergmann D, De Smet I, Sozzani R, Weijers D, Brady SM. Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants. Ann Bot 2014; 113:1083-1105. [PMID: 24825294 PMCID: PMC4030820 DOI: 10.1093/aob/mcu065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development. SCOPE This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. CONCLUSIONS Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Adam Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dominique C. Bergmann
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands
| | - Siobhan M. Brady
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
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21
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Abstract
C(4) photosynthesis occurs in the most productive crops and vegetation on the planet, and has become widespread because it allows increased rates of photosynthesis compared with the ancestral C(3) pathway. Leaves of C(4) plants typically possess complicated alterations to photosynthesis, such that its reactions are compartmented between mesophyll and bundle sheath cells. Despite its complexity, the C(4) pathway has arisen independently in 62 separate lineages of land plants, and so represents one of the most striking examples of convergent evolution known. We demonstrate that elements in untranslated regions (UTRs) of multiple genes important for C(4) photosynthesis contribute to the metabolic compartmentalization characteristic of a C(4) leaf. Either the 5' or the 3' UTR is sufficient for cell specificity, indicating that functional redundancy underlies this key aspect of C(4) gene expression. Furthermore, we show that orthologous PPDK and CA genes from the C(3) plant Arabidopsis thaliana are primed for recruitment into the C(4) pathway. Elements sufficient for M-cell specificity in C(4) leaves are also present in both the 5' and 3' UTRs of these C(3) A. thaliana genes. These data indicate functional latency within the UTRs of genes from C(3) species that have been recruited into the C(4) pathway. The repeated recruitment of pre-existing cis-elements in C(3) genes may have facilitated the evolution of C(4) photosynthesis. These data also highlight the importance of alterations in trans in producing a functional C(4) leaf, and so provide insight into both the evolution and molecular basis of this important type of photosynthesis.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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22
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Kajala K, Covshoff S, Karki S, Woodfield H, Tolley BJ, Dionora MJA, Mogul RT, Mabilangan AE, Danila FR, Hibberd JM, Quick WP. Strategies for engineering a two-celled C(4) photosynthetic pathway into rice. J Exp Bot 2011; 62:3001-10. [PMID: 21335436 DOI: 10.1093/jxb/err022] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Every day almost one billion people suffer from chronic hunger, and the situation is expected to deteriorate with a projected population growth to 9 billion worldwide by 2050. In order to provide adequate nutrition into the future, rice yields in Asia need to increase by 60%, a change that may be achieved by introduction of the C(4) photosynthetic cycle into rice. The international C(4) Rice Consortium was founded in order to test the feasibility of installing the C(4) engine into rice. This review provides an update on two of the many approaches employed by the C(4) Rice Consortium: namely, metabolic C(4) engineering and identification of determinants of leaf anatomy by mutant screens. The aim of the metabolic C(4) engineering approach is to generate a two-celled C(4) shuttle in rice by expressing the classical enzymes of the NADP-ME C(4) cycle in a cell-appropriate manner. The aim is also to restrict RuBisCO and glycine decarboxylase expression to the bundle sheath (BS) cells of rice in a C(4)-like fashion by specifically down-regulating their expression in rice mesophyll (M) cells. In addition to the changes in biochemistry, two-celled C(4) species show a convergence in leaf anatomy that include increased vein density and reduced numbers of M cells between veins. By screening rice activation-tagged lines and loss-of-function sorghum mutants we endeavour to identify genes controlling these key traits.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge CB2 3EA, Cambridge, UK
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23
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Brown NJ, Newell CA, Stanley S, Chen JE, Perrin AJ, Kajala K, Hibberd JM. Independent and Parallel Recruitment of Preexisting Mechanisms Underlying C4 Photosynthesis. Science 2011; 331:1436-9. [DOI: 10.1126/science.1201248] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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24
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Bräutigam A, Kajala K, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Maß J, Lercher MJ, Westhoff P, Hibberd JM, Weber AP. An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiol 2011; 155:142-56. [PMID: 20543093 PMCID: PMC3075794 DOI: 10.1104/pp.110.159442] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/09/2010] [Indexed: 05/18/2023]
Abstract
C(4) photosynthesis involves alterations to the biochemistry, cell biology, and development of leaves. Together, these modifications increase the efficiency of photosynthesis, and despite the apparent complexity of the pathway, it has evolved at least 45 times independently within the angiosperms. To provide insight into the extent to which gene expression is altered between C(3) and C(4) leaves, and to identify candidates associated with the C(4) pathway, we used massively parallel mRNA sequencing of closely related C(3) (Cleome spinosa) and C(4) (Cleome gynandra) species. Gene annotation was facilitated by the phylogenetic proximity of Cleome and Arabidopsis (Arabidopsis thaliana). Up to 603 transcripts differ in abundance between these C(3) and C(4) leaves. These include 17 transcription factors, putative transport proteins, as well as genes that in Arabidopsis are implicated in chloroplast movement and expansion, plasmodesmatal connectivity, and cell wall modification. These are all characteristics known to alter in a C(4) leaf but that previously had remained undefined at the molecular level. We also document large shifts in overall transcription profiles for selected functional classes. Our approach defines the extent to which transcript abundance in these C(3) and C(4) leaves differs, provides a blueprint for the NAD-malic enzyme C(4) pathway operating in a dicotyledon, and furthermore identifies potential regulators. We anticipate that comparative transcriptomics of closely related species will provide deep insight into the evolution of other complex traits.
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25
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Brown NJ, Palmer BG, Stanley S, Hajaji H, Janacek SH, Astley HM, Parsley K, Kajala K, Quick WP, Trenkamp S, Fernie AR, Maurino VG, Hibberd JM. C acid decarboxylases required for C photosynthesis are active in the mid-vein of the C species Arabidopsis thaliana, and are important in sugar and amino acid metabolism. Plant J 2010; 61:122-33. [PMID: 19807880 DOI: 10.1111/j.1365-313x.2009.04040.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cells associated with veins of petioles of C(3) tobacco possess high activities of the decarboxylase enzymes required in C(4) photosynthesis. It is not clear whether this is the case in other C(3) species, nor whether these enzymes provide precursors for specific biosynthetic pathways. Here, we investigate the activity of C(4) acid decarboxylases in the mid-vein of Arabidopsis, identify regulatory regions sufficient for this activity, and determine the impact of removing individual isoforms of each protein on mid-vein metabolite profiles. This showed that radiolabelled malate and bicarbonate fed to the xylem stream were incorporated into soluble and insoluble material in the mid-vein of Arabidopsis leaves. Compared with the leaf lamina, mid-veins possessed high activities of NADP-dependent malic enzyme (NADP-ME), NAD-dependent malic enzyme (NAD-ME) and phosphoenolpyruvate carboxykinase (PEPCK). Transcripts derived from both NAD-ME, one PCK and two of the four NADP-ME genes were detectable in these veinal cells. The promoters of each decarboxylase gene were sufficient for expression in mid-veins. Analysis of insertional mutants revealed that cytosolic NADP-ME2 is responsible for 80% of NADP-ME activity in mid-veins. Removing individual decarboxylases affected the abundance of amino acids derived from pyruvate and phosphoenolpyruvate. Reducing cytosolic NADP-ME activity preferentially affected the sugar content, whereas abolishing NAD-ME affected both the amino acid and the glucosamine content of mid-veins.
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Affiliation(s)
- Naomi J Brown
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, CB2 3EA, UK
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