1
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Pri-Tal O, Sun Y, Dadras A, Fürst-Jansen JMR, Zimran G, Michaeli D, Wijerathna-Yapa A, Shpilman M, Merilo E, Yarmolinsky D, Efroni I, de Vries J, Kollist H, Mosquna A. Constitutive activation of ABA receptors in Arabidopsis reveals unique regulatory circuitries. New Phytol 2024; 241:703-714. [PMID: 37915144 DOI: 10.1111/nph.19363] [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: 08/20/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Abscisic acid (ABA) is best known for regulating the responses to abiotic stressors. Thus, applications of ABA signaling pathways are considered promising targets for securing yield under stress. ABA levels rise in response to abiotic stress, mounting physiological and metabolic responses that promote plant survival under unfavorable conditions. ABA elicits its effects by binding to a family of soluble receptors found in monomeric and dimeric states, differing in their affinity to ABA and co-receptors. However, the in vivo significance of the biochemical differences between these receptors remains unclear. We took a gain-of-function approach to study receptor-specific functionality. First, we introduced activating mutations that enforce active ABA-bound receptor conformation. We then transformed Arabidopsis ABA-deficient mutants with the constitutive receptors and monitored suppression of the ABA deficiency phenotype. Our findings suggest that PYL4 and PYL5, monomeric ABA receptors, have differential activity in regulating transpiration and transcription of ABA biosynthesis and stress response genes. Through genetic and metabolic data, we demonstrate that PYR1, but not PYL5, is sufficient to activate the ABA positive feedback mechanism. We propose that ABA signaling - from perception to response - flows differently when triggered by different PYLs, due to tissue and transcription barriers, thus resulting in distinct circuitries.
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Affiliation(s)
- Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Yufei Sun
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Armin Dadras
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Daphna Michaeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Akila Wijerathna-Yapa
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Michal Shpilman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | | | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtsr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
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2
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Israeli A, Schubert R, Man N, Teboul N, Serrani Yarce JC, Rosowski EE, Wu MF, Levy M, Efroni I, Ljung K, Hause B, Reed JW, Ori N. Modulating auxin response stabilizes tomato fruit set. Plant Physiol 2023; 192:2336-2355. [PMID: 37032117 PMCID: PMC10315294 DOI: 10.1093/plphys/kiad205] [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] [Received: 01/19/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/01/2023]
Abstract
Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here, we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.
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Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Ramona Schubert
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Nave Man
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Naama Teboul
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | | | - Emily E Rosowski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Miin-Feng Wu
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Matan Levy
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 901 83, Sweden
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Jason W Reed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel
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3
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Modrego A, Pasternak T, Omary M, Albacete A, Cano A, Pérez-Pérez JM, Efroni I. Mapping of the Classical Mutation rosette Highlights a Role for Calcium in Wound-Induced Rooting. Plant Cell Physiol 2023; 64:152-164. [PMID: 36398993 DOI: 10.1093/pcp/pcac163] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Removal of the root system induces the formation of new roots from the remaining shoot. This process is primarily controlled by the phytohormone auxin, which interacts with other signals in a yet unresolved manner. Here, we study the classical tomato mutation rosette (ro), which lacks shoot-borne roots. ro mutants were severely inhibited in formation of wound-induced roots (WiRs) and had reduced auxin transport rates. We mapped ro to the tomato ortholog of the Arabidopsis thaliana BIG and the mammalians UBR4/p600. RO/BIG is a large protein of unknown biochemical function. In A. thaliana, BIG was implicated in regulating auxin transport and calcium homeostasis. We show that exogenous calcium inhibits WiR formation in tomato and A. thaliana ro/big mutants. Exogenous calcium antagonized the root-promoting effects of the auxin indole-3-acetic-acid but not of 2,4-dichlorophenoxyacetic acid, an auxin analog that is not recognized by the polar transport machinery, and accumulation of the auxin transporter PIN-FORMED1 (PIN1) was sensitive to calcium levels in the ro/big mutants. Consistent with a role for calcium in mediating auxin transport, both ro/big mutants and calcium-treated wild-type plants were hypersensitive to treatment with polar auxin transport inhibitors. Subcellular localization of BIG suggests that, like its mammalian ortholog, it is associated with the endoplasmic reticulum. Analysis of subcellular morphology revealed that ro/big mutants exhibited disruption in cytoplasmic streaming. We suggest that RO/BIG maintains auxin flow by stabilizing PIN membrane localization, possibly by attenuating the inhibitory effect of Ca2+ on cytoplasmic streaming.
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Affiliation(s)
- Abelardo Modrego
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Taras Pasternak
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche 03202, Spain
| | - Moutasem Omary
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Alfonso Albacete
- Departamento de Nutrición Vegetal, CEBAS-CSIC, Murcia 30100, Spain
| | - Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia 30100, Spain
| | | | - Idan Efroni
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
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4
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Omary M, Matosevich R, Efroni I. Systemic control of plant regeneration and wound repair. New Phytol 2023; 237:408-413. [PMID: 36101501 PMCID: PMC10092612 DOI: 10.1111/nph.18487] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Plants have a broad capacity to regenerate damaged organs. The study of wounding in multiple developmental systems has uncovered many of the molecular properties underlying plants' competence for regeneration at the local cellular level. However, in nature, wounding is rarely localized to one place, and plants need to coordinate regeneration responses at multiple tissues with environmental conditions and their physiological state. Here, we review the evidence for systemic signals that regulate regeneration on a plant-wide level. We focus on the role of auxin and sugars as short- and long-range signals in natural wounding contexts and discuss the varied origin of these signals in different regeneration scenarios. Together, this evidence calls for a broader, system-wide view of plant regeneration competence.
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Affiliation(s)
- Moutasem Omary
- The Institute of Plant Sciences, Faculty of AgricultureThe Hebrew UniversityRehovot761000Israel
| | - Rotem Matosevich
- The Institute of Plant Sciences, Faculty of AgricultureThe Hebrew UniversityRehovot761000Israel
| | - Idan Efroni
- The Institute of Plant Sciences, Faculty of AgricultureThe Hebrew UniversityRehovot761000Israel
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5
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Keren-Keiserman A, Shtern A, Levy M, Chalupowicz D, Furumizu C, Alvarez JP, Amsalem Z, Arazi T, Alkalai-Tuvia S, Efroni I, Ori N, Bowman JL, Fallik E, Goldshmidt A. CLASS-II KNOX genes coordinate spatial and temporal ripening in tomato. Plant Physiol 2022; 190:657-668. [PMID: 35703985 PMCID: PMC9434150 DOI: 10.1093/plphys/kiac290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 05/13/2023]
Abstract
Fruits can be divided into dry and fleshy types. Dry fruits mature through senescence and fleshy fruits through ripening. Previous studies have indicated that partially common molecular networks could govern fruit maturation in these different fruit types. However, the nature of such networks remains obscure. CLASS-II KNOX genes were shown to regulate the senescence of the Arabidopsis (Arabidopsis thaliana) dry fruits, the siliques, but their roles in fleshy-fruit development are unknown. Here, we investigated the roles of the tomato (Solanum lycopersicum) CLASS-II KNOX (TKN-II) genes in fleshy fruit ripening using knockout alleles of individual genes and an artificial microRNA line (35S:amiR-TKN-II) simultaneously targeting all genes. 35S:amiR-TKN-II plants, as well as a subset of tkn-II single and double mutants, have smaller fruits. Strikingly, the 35S:amiR-TKN-II and tknII3 tknII7/+ fruits showed early ripening of the locular domain while their pericarp ripening was stalled. Further examination of the ripening marker-gene RIPENING INHIBITOR (RIN) expression and 35S:amiR-TKN-II rin-1 mutant fruits suggested that TKN-II genes arrest RIN activity at the locular domain and promote it in the pericarp. These findings imply that CLASS-II KNOX genes redundantly coordinate maturation in both dry and fleshy fruits. In tomato, these genes also control spatial patterns of fruit ripening, utilizing differential regulation of RIN activity at different fruit domains.
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Affiliation(s)
- Alexandra Keren-Keiserman
- Institute of Plant Sciences, ARO, Volcani Institute, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Amit Shtern
- Institute of Plant Sciences, ARO, Volcani Institute, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Matan Levy
- Department of Plant Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel
| | - Daniel Chalupowicz
- Institute of Postharvest and Food Sciences, ARO, Volcani Institute, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | | | - John Paul Alvarez
- School of Biological Sciences, Monash University, Wellington Road, Clayton, Melbourne, Victoria 3800, Australia
| | - Ziva Amsalem
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tzahi Arazi
- Institute of Plant Sciences, ARO, Volcani Institute, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Sharon Alkalai-Tuvia
- Institute of Postharvest and Food Sciences, ARO, Volcani Institute, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Idan Efroni
- Department of Plant Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel
| | - Naomi Ori
- Department of Plant Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel
| | - John L Bowman
- School of Biological Sciences, Monash University, Wellington Road, Clayton, Melbourne, Victoria 3800, Australia
| | - Elazar Fallik
- Institute of Postharvest and Food Sciences, ARO, Volcani Institute, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
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6
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Matosevich R, Cohen I, Gil-Yarom N, Modrego A, Friedlander-Shani L, Verna C, Scarpella E, Efroni I. Author Correction: Local auxin biosynthesis is required for root regeneration after wounding. Nat Plants 2022; 8:857. [PMID: 35788167 DOI: 10.1038/s41477-022-01205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Rotem Matosevich
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Itay Cohen
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Abelardo Modrego
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Carla Verna
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- California Institute of Technology, Pasadena, CA, USA
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
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7
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Abstract
Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.
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Affiliation(s)
- Moutasem Omary
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Yahav
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Evyatar Steiner
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Idan Efroni
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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8
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Abstract
Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.
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Affiliation(s)
- Moutasem Omary
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Yahav
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Evyatar Steiner
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Idan Efroni
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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9
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Ackerman-Lavert M, Fridman Y, Matosevich R, Khandal H, Friedlander-Shani L, Vragović K, Ben El R, Horev G, Tarkowská D, Efroni I, Savaldi-Goldstein S. Auxin requirements for a meristematic state in roots depend on a dual brassinosteroid function. Curr Biol 2021; 31:4462-4472.e6. [PMID: 34418341 DOI: 10.1016/j.cub.2021.07.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/09/2020] [Revised: 05/24/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Root meristem organization is maintained by an interplay between hormone signaling pathways that both interpret and determine their accumulation and distribution. The interacting hormones Brassinosteroids (BR) and auxin control the number of meristematic cells in the Arabidopsis root. BR was reported both to promote auxin signaling input and to repress auxin signaling output. Whether these contradicting molecular outcomes co-occur and what their significance in meristem function is remain unclear. Here, we established a dual effect of BR on auxin, with BR simultaneously promoting auxin biosynthesis and repressing auxin transcriptional output, which is essential for meristem maintenance. Blocking BR-induced auxin synthesis resulted in rapid BR-mediated meristem loss. Conversely, plants with reduced BR levels were resistant to a critical loss of auxin biosynthesis, maintaining their meristem morphology. In agreement, injured root meristems, which rely solely on local auxin synthesis, regenerated when both auxin and BR synthesis were inhibited. Use of BIN2 as a tool to selectively inhibit BR signaling yielded meristems with distinct phenotypes depending on the perturbed tissue: meristem reminiscent either of BR-deficient mutants or of high BR exposure. This enabled mapping of the BR-auxin interaction that maintains the meristem to the outer epidermis and lateral root cap tissues and demonstrated the essentiality of BR signaling in these tissues for meristem response to BR. BR activity in internal tissues however, proved necessary to control BR levels. Together, we demonstrate a basis for inter-tissue coordination and how a critical ratio between these hormones determines the meristematic state.
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Affiliation(s)
- M Ackerman-Lavert
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Y Fridman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - R Matosevich
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - H Khandal
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - L Friedlander-Shani
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - K Vragović
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - R Ben El
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - G Horev
- Lorey I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - D Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Olomouc, Czech Republic
| | - I Efroni
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - S Savaldi-Goldstein
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
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10
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Abstract
Since its discovery by F.A.L Clowes, extensive research has been dedicated to identifying the functions of the quiescent center (QC). One of the earliest hypotheses was that it serves a key role in regeneration of the root meristem. Recent works provided support for this hypothesis and began to elucidate the molecular mechanisms underlying this phenomenon. There are two scenarios to consider when assessing the role of the QC in regeneration: one, when the damage leaves the QC intact; and the other, when the QC itself is destroyed. In the first scenario, multiple factors are recruited to activate QC cell division in order to replace damaged cells, but whether the QC has a role in the second scenario is less clear. Both using gene expression studies and following the cell division pattern have shown that the QC is assembled gradually, only to appear as a coherent identity late in regeneration. Similar late emergence of the QC was observed during the de novo formation of the lateral root meristem. These observations can lead to the conclusion that the QC has no role in regeneration. However, activities normally occurring in QC cells, such as local auxin biosynthesis, are still found during regeneration but occur in different cells in the regenerating meristem. Thus, we explore an alternative hypothesis, that following destruction of the QC, QC-related gene activity is temporarily distributed to other cells in the regenerating meristem, and only coalesce into a distinct cell identity when regeneration is complete.
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Affiliation(s)
- Rotem Matosevich
- The Institute of Plant Sciences, Faculty of Agriculture, The Hebrew University, Rehovot, Israel
| | - Idan Efroni
- The Institute of Plant Sciences, Faculty of Agriculture, The Hebrew University, Rehovot, Israel
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11
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Hendelman A, Zebell S, Rodriguez-Leal D, Dukler N, Robitaille G, Wu X, Kostyun J, Tal L, Wang P, Bartlett ME, Eshed Y, Efroni I, Lippman ZB. Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell 2021; 184:1724-1739.e16. [PMID: 33667348 DOI: 10.1016/j.cell.2021.02.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generate a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identifies the regions responsible for this pleiotropic activity, the functions of which are conserved in groundcherry, a tomato relative. Mimicking these alleles in Arabidopsis, distantly related to tomato and groundcherry, reveals new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.
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Affiliation(s)
- Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Noah Dukler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xuelin Wu
- The Salk Institute for Biological Research, San Diego, CA, USA
| | - Jamie Kostyun
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Lior Tal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peipei Wang
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel
| | | | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel.
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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12
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Israeli A, Ben-Herzel O, Burko Y, Shwartz I, Ben-Gera H, Harpaz-Saad S, Bar M, Efroni I, Ori N. Coordination of differentiation rate and local patterning in compound-leaf development. New Phytol 2021; 229:3558-3572. [PMID: 33259078 DOI: 10.1111/nph.17124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/17/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The variability in leaf form in nature is immense. Leaf patterning occurs by differential growth, taking place during a limited window of morphogenetic activity at the leaf marginal meristem. While many regulators have been implicated in the designation of the morphogenetic window and in leaf patterning, how these effectors interact to generate a particular form is still not well understood. We investigated the interaction among different effectors of tomato (Solanum lycopersicum) compound-leaf development, using genetic and molecular analyses. Mutations in the tomato auxin response factor SlARF5/SlMP, which normally promotes leaflet formation, suppressed the increased leaf complexity of mutants with extended morphogenetic window. Impaired activity of the NAC/CUC transcription factor GOBLET (GOB), which specifies leaflet boundaries, also reduced leaf complexity in these backgrounds. Analysis of genetic interactions showed that the patterning factors SlMP, GOB and the MYB transcription factor LYRATE (LYR) coordinately regulate leaf patterning by modulating in parallel different aspects of leaflet formation and shaping. This work places an array of developmental regulators in a morphogenetic context. It reveals how organ-level differentiation rate and local growth are coordinated to sculpture an organ. These concepts are applicable to the coordination of pattering and differentiation in other species and developmental processes.
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Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Ori Ben-Herzel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Yogev Burko
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ido Shwartz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Hadas Ben-Gera
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, PO Box 102, Ramat Yishay, 30095, Israel
| | - Smadar Harpaz-Saad
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Maya Bar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, 7505101, Israel
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
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13
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Matosevich R, Cohen I, Gil-Yarom N, Modrego A, Friedlander-Shani L, Verna C, Scarpella E, Efroni I. Local auxin biosynthesis is required for root regeneration after wounding. Nat Plants 2020; 6:1020-1030. [PMID: 32747761 DOI: 10.1038/s41477-020-0737-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 07/02/2020] [Indexed: 05/21/2023]
Abstract
The root meristem can regenerate following removal of its stem-cell niche by recruitment of remnant cells from the stump. Regeneration is initiated by rapid accumulation of auxin near the injury site but the source of this auxin is unknown. Here, we show that auxin accumulation arises from the activity of multiple auxin biosynthetic sources that are newly specified near the cut site and that their continuous activity is required for the regeneration process. Auxin synthesis is highly localized while PIN-mediated transport is dispensable for auxin accumulation and tip regeneration. Roots lacking the activity of the regeneration competence factor ERF115, or that are dissected at a zone of low regeneration potential, fail to activate local auxin sources. Remarkably, restoring auxin supply is sufficient to confer regeneration capacity to these recalcitrant tissues. We suggest that regeneration competence relies on the ability to specify new local auxin sources in a precise temporal pattern.
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Affiliation(s)
- Rotem Matosevich
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Itay Cohen
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Abelardo Modrego
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Carla Verna
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- California Institute of Technology, Pasadena, CA, USA
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
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14
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Radhakrishnan D, Shanmukhan AP, Kareem A, Aiyaz M, Varapparambathu V, Toms A, Kerstens M, Valsakumar D, Landge AN, Shaji A, Mathew MK, Sawchuk MG, Scarpella E, Krizek BA, Efroni I, Mähönen AP, Willemsen V, Scheres B, Prasad K. A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context. Development 2020; 147:dev185710. [PMID: 32108025 DOI: 10.1242/dev.185710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 10/15/2019] [Accepted: 02/17/2020] [Indexed: 03/01/2024]
Abstract
Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.
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Affiliation(s)
- Dhanya Radhakrishnan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | | | - Abdul Kareem
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Mohammed Aiyaz
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Vijina Varapparambathu
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Ashna Toms
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Merijn Kerstens
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Devisree Valsakumar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Amit N Landge
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Anil Shaji
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Mathew K Mathew
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, 15, Bengaluru, 560065, India
| | - Megan G Sawchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Beth A Krizek
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot 76100, Israel
| | - Ari Pekka Mähönen
- Institute of Biotechnology HiLIFE, University of Helsinki, 00014 Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
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15
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Lieberman-Lazarovich M, Yahav C, Israeli A, Efroni I. Deep Conservation of cis-Element Variants Regulating Plant Hormonal Responses. Plant Cell 2019; 31:2559-2572. [PMID: 31467248 PMCID: PMC6881130 DOI: 10.1105/tpc.19.00129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/27/2019] [Indexed: 05/14/2023]
Abstract
Phytohormones regulate many aspects of plant life by activating transcription factors (TFs) that bind sequence-specific response elements (REs) in regulatory regions of target genes. Despite their short length, REs are degenerate, with a core of just 3 to 4 bp. This degeneracy is paradoxical, as it reduces specificity and REs are extremely common in the genome. To study whether RE degeneracy might serve a biological function, we developed an algorithm for the detection of regulatory sequence conservation and applied it to phytohormone REs in 45 angiosperms. Surprisingly, we found that specific RE variants are highly conserved in core hormone response genes. Experimental evidence showed that specific variants act to regulate the magnitude and spatial profile of hormonal response in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum). Our results suggest that hormone-regulated TFs bind a spectrum of REs, each coding for a distinct transcriptional response profile. Our approach has implications for precise genome editing and for rational promoter design.
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Affiliation(s)
- Michal Lieberman-Lazarovich
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Chen Yahav
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Alon Israeli
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
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16
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Mello A, Efroni I, Rahni R, Birnbaum KD. The Selaginella rhizophore has a unique transcriptional identity compared to root and shoot meristems. New Phytol 2018; 222:10.1111/nph.15630. [PMID: 30614003 PMCID: PMC6559876 DOI: 10.1111/nph.15630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/30/2018] [Indexed: 05/12/2023]
Abstract
The genus Selaginella resides in an early branch of the land plant lineage that possesses a vasculature and roots. The majority of the Selaginella root system is shoot borne and emerges through a distinctive structure known as the rhizophore, the organ identity of which has been a long-debated question. The rhizophore of Selaginella moellendorffii - a model for the lycophytes - shows plasticity to develop into a root or shoot up until 8 d after angle meristem emergence, after which it is committed to root fate. We subsequently use morphology and plasticity to define the stage of rhizophore identity. Transcriptomic analysis of the rhizophore during its plastic stage reveals that, despite some resemblance to the root meristem, rhizophore gene expression patterns are largely distinct from both shoot and root meristems. Based on this transcriptomic analysis and on historical anatomical work, we conclude that the rhizophore is a distinct organ with unique features.
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Affiliation(s)
- Alison Mello
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, N.Y. 10003, USA
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, POB 12, Rehovot 76100, Israel
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, N.Y. 10003, USA
| | - Kenneth D. Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, N.Y. 10003, USA
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17
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Efroni I, Prasad K. Insights into the art of recreation. Dev Biol 2018; 442:1-2. [PMID: 30213362 DOI: 10.1016/j.ydbio.2018.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Idan Efroni
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.Box 12, Rehovot 76100, Israel.
| | - Kalika Prasad
- Indian Institute of Science Education and Research, School of Biology, Maruthamala PO, Vithura, Thiruvananthapuram 69551, India.
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18
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Abstract
Multicellular organisms develop from a single cell that proliferates to form different cell types with specialized functions. Sixty years ago, Waddington suggested the 'epigenetic landscape' as a useful metaphor for the process. According to this view, cells move through a rugged identity space along genetically encoded trajectories, until arriving at one of the possible final fates. In plants in particular, these trajectories have strong spatial correlates, as cell identity is intimately linked to its relative position within the plant. During regeneration, however, positional signals are severely disrupted and differentiated cells are able to undergo rapid non-canonical identity changes. Moreover, while pluripotent properties have long been ascribed to plant cells, the introduction of induced pluripotent stem cells in animal studies suggests such plasticity may not be unique to plants. As a result, current concepts of differentiation as a gradual and hierarchical process are being reformulated across biological fields. Traditional studies of plant regeneration have placed strong emphasis on the emergence of patterns and tissue organization, and information regarding the events occurring at the level of individual cells is only now beginning to emerge. Here, I review the historical and current concepts of cell identity and identity transitions, and discuss how new views and tools may instruct the future understanding of differentiation and plant regeneration.
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Affiliation(s)
- Idan Efroni
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot, Israel
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19
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Rahni R, Efroni I, Birnbaum KD. A Case for Distributed Control of Local Stem Cell Behavior in Plants. Dev Cell 2017; 38:635-42. [PMID: 27676436 DOI: 10.1016/j.devcel.2016.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/11/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
Abstract
The root meristem has a centrally located group of mitotically quiescent cells, to which current models assign a stem cell organizer function. However, evidence is emerging for decentralized control of stem cell activity, whereby self-renewing behavior emerges from the lack of cell displacement at the border of opposing differentiation gradients. We term this a "stagnation" model due to its reliance on passive mechanics. The position of stem cells is established by two opposing axes that reciprocally control each other's differentiation. Such broad tissue organization programs would allow plants, like some animal systems, to rapidly reconstitute stem cells from non-stem-cell tissues.
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Affiliation(s)
- Ramin Rahni
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot 76100, Israel
| | - Kenneth D Birnbaum
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
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20
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Alvarez JP, Furumizu C, Efroni I, Eshed Y, Bowman JL. Active suppression of a leaf meristem orchestrates determinate leaf growth. eLife 2016; 5. [PMID: 27710768 PMCID: PMC5096885 DOI: 10.7554/elife.15023] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/30/2016] [Indexed: 12/29/2022] Open
Abstract
Leaves are flat determinate organs derived from indeterminate shoot apical meristems. The presence of a specific leaf meristem is debated, as anatomical features typical of meristems are not present in leaves. Here we demonstrate that multiple NGATHA (NGA) and CINCINNATA-class-TCP (CIN-TCP) transcription factors act redundantly, shortly after leaf initiation, to gradually restrict the activity of a leaf meristem in Arabidopsis thaliana to marginal and basal domains, and that their absence confers persistent marginal growth to leaves, cotyledons and floral organs. Following primordia initiation, the restriction of the broadly acting leaf meristem to the margins is mediated by the juxtaposition of adaxial and abaxial domains and maintained by WOX homeobox transcription factors, whereas other marginal elaboration genes are dispensable for its maintenance. This genetic framework parallels the morphogenetic program of shoot apical meristems and may represent a relic of an ancestral shoot system from which seed plant leaves evolved. DOI:http://dx.doi.org/10.7554/eLife.15023.001
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Affiliation(s)
- John Paul Alvarez
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Chihiro Furumizu
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yuval Eshed
- Department of Plant and environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Australia.,Department of Plant Biology, University of California, Davis, Davis, California, United States
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21
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Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD. Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions. Cell 2016; 165:1721-1733. [PMID: 27212234 DOI: 10.1016/j.cell.2016.04.046] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/02/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023]
Abstract
Plant roots can regenerate after excision of their tip, including the stem cell niche. To determine which developmental program mediates such repair, we applied a combination of lineage tracing, single-cell RNA sequencing, and marker analysis to test different models of tissue reassembly. We show that multiple cell types can reconstitute stem cells, demonstrating the latent potential of untreated plant cells. The transcriptome of regenerating cells prior to stem cell activation resembles that of an embryonic root progenitor. Regeneration defects are more severe in embryonic than in adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirror their embryonic dynamics and manipulation of both hormones alters the position of new tissues and stem cell niche markers. Our findings suggest that plant root regeneration follows, on a larger scale, the developmental stages of embryonic patterning and is guided by spatial information provided by complementary hormone domains.
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Affiliation(s)
- Idan Efroni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Alison Mello
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Tal Nawy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Nicholas DelRose
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | | | - Rahul Satija
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
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22
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Abstract
Single-cell transcriptomics has been employed in a growing number of animal studies, but the technique has yet to be widely used in plants. Nonetheless, early studies indicate that single-cell RNA-seq protocols developed for animal cells produce informative datasets in plants. We argue that single-cell transcriptomics has the potential to provide a new perspective on plant problems, such as the nature of the stem cells or initials, the plasticity of plant cells, and the extent of localized cellular responses to environmental inputs. Single-cell experimental outputs require different analytical approaches compared with pooled cell profiles and new tools tailored to single-cell assays are being developed. Here, we highlight promising new single-cell profiling approaches, their limitations as applied to plants, and their potential to address fundamental questions in plant biology.
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Affiliation(s)
- Idan Efroni
- The Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.,Present address: The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot, 76100, Israel
| | - Kenneth D Birnbaum
- The Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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23
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Efroni I, Ip PL, Nawy T, Mello A, Birnbaum KD. Quantification of cell identity from single-cell gene expression profiles. Genome Biol 2015; 16:9. [PMID: 25608970 PMCID: PMC4354993 DOI: 10.1186/s13059-015-0580-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/31/2014] [Indexed: 01/04/2023] Open
Abstract
The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify identities from single-cell RNA-seq profiles, accurately classifying cells from Arabidopsis root tips and human glioblastoma tumors. We apply our approach to single cells captured from regenerating roots following tip excision. Our technique exposes a previously uncharacterized transient collapse of identity distant from the injury site, demonstrating the biological relevance of a quantitative cell identity index.
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Affiliation(s)
- Idan Efroni
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA.
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA.
| | - Tal Nawy
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA.
| | - Alison Mello
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA.
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA.
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24
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Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G. TARGET: a transient transformation system for genome-wide transcription factor target discovery. Mol Plant 2013; 6:978-80. [PMID: 23335732 PMCID: PMC3660954 DOI: 10.1093/mp/sst010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Bastiaan O.R. Bargmann
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Amy Marshall-Colon
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Idan Efroni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sandrine Ruffel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France
| | - Kenneth D. Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Gloria M. Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- To whom correspondence should be addressed. G.K. E-mail , , tel. +0(33)499612518. G.M.C. E-mail
| | - Gabriel Krouk
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France
- To whom correspondence should be addressed. G.K. E-mail , , tel. +0(33)499612518. G.M.C. E-mail
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Efroni I, Han SK, Kim HJ, Wu MF, Steiner E, Birnbaum KD, Hong JC, Eshed Y, Wagner D. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev Cell 2013; 24:438-45. [PMID: 23449474 DOI: 10.1016/j.devcel.2013.01.019] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [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: 05/01/2011] [Revised: 11/07/2012] [Accepted: 01/23/2013] [Indexed: 11/18/2022]
Abstract
Plant shoots display indeterminate growth, while their evolutionary decedents, the leaves, are determinate. Determinate leaf growth is conditioned by the CIN-TCP transcription factors, which promote leaf maturation and are negatively regulated by miR319 in leaf primordia. Here we show that CIN-TCPs reduce leaf sensitivity to cytokinin (CK), a phytohormone implicated in inhibition of differentiation in the shoot. We identify the SWI/SNF chromatin remodeling ATPase BRAHMA (BRM) as a genetic mediator of CIN-TCP activities and CK responses. An interactome screen further revealed that SWI/SNF complex components including BRM preferentially interacted with basic-helix-loop-helix (bHLH) transcription factors and the bHLH-related CIN-TCPs. Indeed, TCP4 and BRM interacted in planta. Both TCP4 and BRM bound the promoter of an inhibitor of CK responses, ARR16, and induced its expression. Reconstituting ARR16 levels in leaves with reduced CIN-TCP activity restored normal growth. Thus, CIN-TCP and BRM together promote determinate leaf growth by stage-specific modification of CK responses.
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Affiliation(s)
- Idan Efroni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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26
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Bargmann BOR, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD. A map of cell type-specific auxin responses. Mol Syst Biol 2013; 9:688. [PMID: 24022006 PMCID: PMC3792342 DOI: 10.1038/msb.2013.40] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/23/2013] [Indexed: 12/31/2022] Open
Abstract
In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.
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Affiliation(s)
- Bastiaan O R Bargmann
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes—Claude Grignon, Montpellier, France
| | - Tal Nawy
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Idan Efroni
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Eilon Shani
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Goh Choe
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Jiří Friml
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | | | - Mark Estelle
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Kenneth D Birnbaum
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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27
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Steiner E, Yanai O, Efroni I, Ori N, Eshed Y, Weiss D. Class I TCPs modulate cytokinin-induced branching and meristematic activity in tomato. Plant Signal Behav 2012; 7:807-10. [PMID: 22751297 PMCID: PMC3583969 DOI: 10.4161/psb.20606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Arabidopsis TCPs are a family of basic helix loop helix (bHLH)-type transcription factors. Previous studies suggested that antagonistic activities of class I TCPs and class II TCPs are correlated with cell proliferation. We have recently shown that the class I TCPs AtTCP14 and AtTCP15 promote typical cytokinin (CK) responses in Arabidopsis, and proposed that they mediate the effect of CK on cell divisions. To further study the role of AtTCP14 and AtTCP15 in plant development, we expressed them in tomato plants. AtTCP14 and AtTCP15-expressing tomato plants were semi-dwarf, had a reduced apical dominance and developed ectopic meristems on leaflet petioles. CK application to tomato seedlings promoted axillary bud outgrowth and this effect was enhanced in the transgenic AtTCP14 and AtTCP15 overexpressing plants. The results of this study extend our previous suggestion that AtTCP14 and AtTCP15 modulate the plant sensitivity to CK.
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Affiliation(s)
- Evyatar Steiner
- Institute of Plant Sciences and Genetics in Agriculture; The Robert H. Smith Faculty of Agriculture; Department of Food and Environment; The Hebrew University of Jerusalem; Rehovot, Israel
| | - Osnat Yanai
- Institute of Plant Sciences and Genetics in Agriculture; The Robert H. Smith Faculty of Agriculture; Department of Food and Environment; The Hebrew University of Jerusalem; Rehovot, Israel
| | - Idan Efroni
- Department of Biology; Center for Genomics and Systems Biology; New York University; New York, NY USA
| | - Naomi Ori
- Institute of Plant Sciences and Genetics in Agriculture; The Robert H. Smith Faculty of Agriculture; Department of Food and Environment; The Hebrew University of Jerusalem; Rehovot, Israel
| | - Yuval Eshed
- Department of Plant Sciences; The Weizmann Institute of Science; Rehovot, Israel
| | - David Weiss
- Institute of Plant Sciences and Genetics in Agriculture; The Robert H. Smith Faculty of Agriculture; Department of Food and Environment; The Hebrew University of Jerusalem; Rehovot, Israel
- Correspondence to: David Weiss,
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Steiner E, Efroni I, Gopalraj M, Saathoff K, Tseng TS, Kieffer M, Eshed Y, Olszewski N, Weiss D. The Arabidopsis O-linked N-acetylglucosamine transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers. Plant Cell 2012; 24:96-108. [PMID: 22267487 PMCID: PMC3289577 DOI: 10.1105/tpc.111.093518] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 12/21/2011] [Accepted: 01/05/2012] [Indexed: 05/18/2023]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) modifications regulate the posttranslational fate of target proteins. The Arabidopsis thaliana O-GlcNAc transferase (OGT) SPINDLY (SPY) suppresses gibberellin signaling and promotes cytokinin (CK) responses by unknown mechanisms. Here, we present evidence that two closely related class I TCP transcription factors, TCP14 and TCP15, act with SPY to promote CK responses. TCP14 and TCP15 interacted with SPY in yeast two-hybrid and in vitro pull-down assays and were O-GlcNAc modified in Escherichia coli by the Arabidopsis OGT, SECRET AGENT. Overexpression of TCP14 severely affected plant development in a SPY-dependent manner and stimulated typical CK morphological responses, as well as the expression of the CK-regulated gene RESPONSE REGULATOR5. TCP14 also promoted the transcriptional activity of the CK-induced mitotic factor CYCLIN B1;2. Whereas TCP14-overexpressing plants were hypersensitive to CK, spy and tcp14 tcp15 double mutant leaves and flowers were hyposensitive to the hormone. Reducing CK levels by overexpressing CK OXIDASE/DEHYDROGENASE3 suppressed the TCP14 overexpression phenotypes, and this suppression was reversed when the plants were treated with exogenous CK. Taken together, we suggest that responses of leaves and flowers to CK are mediated by SPY-dependent TCP14 and TCP15 activities.
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Affiliation(s)
- Evyatar Steiner
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Idan Efroni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Manjula Gopalraj
- Department of Plant Biology and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Katie Saathoff
- Department of Plant Biology and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Tong-Seung Tseng
- Department of Plant Biology and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Martin Kieffer
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yuval Eshed
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Neil Olszewski
- Department of Plant Biology and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - David Weiss
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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29
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Sarojam R, Sappl PG, Goldshmidt A, Efroni I, Floyd SK, Eshed Y, Bowman JL. Differentiating Arabidopsis shoots from leaves by combined YABBY activities. Plant Cell 2010; 22:2113-30. [PMID: 20628155 PMCID: PMC2929102 DOI: 10.1105/tpc.110.075853] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 04/15/2010] [Accepted: 06/17/2010] [Indexed: 05/18/2023]
Abstract
In seed plants, leaves are born on radial shoots, but unlike shoots, they are determinate dorsiventral organs made of flat lamina. YABBY genes are found only in seed plants and in all cases studied are expressed primarily in lateral organs and in a polar manner. Despite their simple expression, Arabidopsis thaliana plants lacking all YABBY gene activities have a wide range of morphological defects in all lateral organs as well as the shoot apical meristem (SAM). Here, we show that leaves lacking all YABBY activities are initiated as dorsiventral appendages but fail to properly activate lamina programs. In particular, the activation of most CINCINNATA-class TCP genes does not commence, SAM-specific programs are reactivated, and a marginal leaf domain is not established. Altered distribution of auxin signaling and the auxin efflux carrier PIN1, highly reduced venation, initiation of multiple cotyledons, and gradual loss of the SAM accompany these defects. We suggest that YABBY functions were recruited to mold modified shoot systems into flat plant appendages by translating organ polarity into lamina-specific programs that include marginal auxin flow and activation of a maturation schedule directing determinate growth.
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Affiliation(s)
- Rajani Sarojam
- Section of Plant Biology, University of California, Davis, California 95616
| | - Pia G. Sappl
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Alexander Goldshmidt
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idan Efroni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sandra K. Floyd
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Yuval Eshed
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - John L. Bowman
- Section of Plant Biology, University of California, Davis, California 95616
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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30
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Efroni I, Eshed Y, Lifschitz E. Morphogenesis of simple and compound leaves: a critical review. Plant Cell 2010; 22:1019-32. [PMID: 20435903 PMCID: PMC2879760 DOI: 10.1105/tpc.109.073601] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 04/09/2010] [Accepted: 04/15/2010] [Indexed: 05/18/2023]
Abstract
The leaves of seed plants evolved from a primitive shoot system and are generated as determinate dorsiventral appendages at the flanks of radial indeterminate shoots. The remarkable variation of leaves has remained a constant source of fascination, and their developmental versatility has provided an advantageous platform to study genetic regulation of subtle, and sometimes transient, morphological changes. Here, we describe how eudicot plants recruited conserved shoot meristematic factors to regulate growth of the basic simple leaf blade and how subsets of these factors are subsequently re-employed to promote and maintain further organogenic potential. By comparing tractable genetic programs of species with different leaf types and evaluating the pros and cons of phylogenetic experimental procedures, we suggest that simple and compound leaves, and, by the same token, leaflets and serrations, are regulated by distinct ontogenetic programs. Finally, florigen, in its capacity as a general growth regulator, is presented as a new upper-tier systemic modulator in the patterning of compound leaves.
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Affiliation(s)
- Idan Efroni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuval Eshed
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Zemach A, Paul LK, Stambolsky P, Efroni I, Rotter V, Grafi G. The C-terminal domain of the Arabidopsis AtMBD7 protein confers strong chromatin binding activity. Exp Cell Res 2009; 315:3554-62. [PMID: 19647732 DOI: 10.1016/j.yexcr.2009.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/26/2009] [Accepted: 07/27/2009] [Indexed: 12/01/2022]
Abstract
The Arabidopsis MBD7 (AtMBD7) - a naturally occurring poly MBD protein - was previously found to be functional in binding methylated-CpG dinucleotides in vitro and localized to highly methylated chromocenters in vivo. Furthermore, AtMBD7 has significantly lower mobility within the nucleus conferred by cooperative activity of its three MBD motifs. Here we show that besides the MBD motifs, AtMBD7 possesses a strong chromatin binding domain located at its C-terminus designated sticky-C (StkC). Mutational analysis showed that a glutamic acid residue near the C-terminus is essential though not sufficient for the StkC function. Further analysis demonstrated that this motif can render nuclear proteins highly immobile both in plant and animal cells, without affecting their native subnuclear localization. Thus, the C-terminal, StkC motif plays an important role in fastening AtMBD7 to its chromosomal, CpG-methylated sites. It may be possible to utilize this motif for fastening nuclear proteins to their chromosomal sites both in plant and animal cells for research and gene therapy applications.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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32
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Alvarez JP, Goldshmidt A, Efroni I, Bowman JL, Eshed Y. The NGATHA distal organ development genes are essential for style specification in Arabidopsis. Plant Cell 2009; 21:1373-93. [PMID: 19435933 PMCID: PMC2700527 DOI: 10.1105/tpc.109.065482] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/25/2009] [Accepted: 04/17/2009] [Indexed: 05/18/2023]
Abstract
Floral organ identities are specified by a few transcription factors that act as master regulators. Subsequently, specification of organ axes programs the distribution of distinct tissue types within the organs that themselves develop unique identities. The C-class, AGAMOUS-clade MADS box genes are primary promoters of the gynoecium, which is divided into a distal style and a subtending ovary along the apical-basal axis. We show that members of a clade of B3 domain transcription factors, NGATHA1 (NGA1) to NGA4, are expressed distally in all lateral organs, and all four have a redundant and essential role in style development. Loss of all four genes results in gynoecia where style is replaced by valve-like projections and a reduction in style-specific SHATTERPROOF1 (SHP1) expression. In agreement, floral misexpression of NGA1 promotes ectopic style and SHP1 expression. STYLISH1, an auxin biosynthesis inducer, conditionally activated NGA genes, which in turn promoted distal expression of other STY genes in a putative positive feedback loop. Inhibited auxin transport or lack of YABBY1 gene activities resulted in a basally expanded style domain and broader expression of NGA genes. We speculate that early gynoecium factors delimit NGA gene response to an auxin-based signal, elicited by STY gene activity, to restrict the activation of style program to a late and distal carpel domain.
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Affiliation(s)
- John Paul Alvarez
- Department of Plant Sciences, Weizman Institute of Science, Rehovot, 76100, Israel
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33
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Efroni I, Blum E, Goldshmidt A, Eshed Y. A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Plant Cell 2008; 20:2293-306. [PMID: 18805992 PMCID: PMC2570723 DOI: 10.1105/tpc.107.057521] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 09/02/2008] [Accepted: 09/09/2008] [Indexed: 05/18/2023]
Abstract
Leaf development has been monitored chiefly by following anatomical markers. Analysis of transcriptome dynamics during leaf maturation revealed multiple expression patterns that rise or fall with age or that display age-specific peaks. These were used to formulate a digital differentiation index (DDI) based on a set of selected markers with informative expression during leaf ontogeny. The leaf-based DDI reliably predicted the developmental state of leaf samples from diverse sources and was independent of mitotic cell division transcripts or propensity of specific cell types. When calibrated by informative root markers, the same algorithm accurately diagnosed dissected root samples. We used the DDI to characterize plants with reduced activities of multiple CINCINNATA (CIN)-TCP (TEOSINTE BRANCHED1, CYCLOIDEA, PCF) growth regulators. These plants had giant curled leaves made up of small cells with abnormal shape, low DDI scores, and low expression of mitosis markers, depicting the primary role of CIN-TCPs as promoters of differentiation. Delayed activity of several CIN-TCPs resulted in abnormally large but flat leaves with regular cells. The application of DDI has therefore portrayed the CIN-TCPs as heterochronic regulators that permit the development of a flexible and robust leaf form through an ordered and protracted maturation schedule.
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Affiliation(s)
- Idan Efroni
- Department of Plant Sciences, Weizman Institute of Science, Rehovot 76100, Israel
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34
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Ori N, Cohen AR, Etzioni A, Brand A, Yanai O, Shleizer S, Menda N, Amsellem Z, Efroni I, Pekker I, Alvarez JP, Blum E, Zamir D, Eshed Y. Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat Genet 2007; 39:787-91. [PMID: 17486095 DOI: 10.1038/ng2036] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 04/13/2007] [Indexed: 11/09/2022]
Abstract
Plant leaves show pronounced plasticity of size and form. In the classical, partially dominant mutation Lanceolate (La), the large compound leaves of tomato (Solanum lycopersicum) are converted into small simple ones. We show that LA encodes a transcription factor from the TCP family containing an miR319-binding site. Five independent La isolates are gain-of-function alleles that result from point mutations within the miR319-binding site and confer partial resistance of the La transcripts to microRNA (miRNA)-directed inhibition. The reduced sensitivity to miRNA regulation leads to elevated LA expression in very young La leaf primordia and to precocious differentiation of leaf margins. In contrast, downregulation of several LA-like genes using ectopic expression of miR319 resulted in larger leaflets and continuous growth of leaf margins. Our results imply that regulation of LA by miR319 defines a flexible window of morphogenetic competence along the developing leaf margin that is required for leaf elaboration.
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Affiliation(s)
- Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
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35
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Bloch D, Lavy M, Efrat Y, Efroni I, Bracha-Drori K, Abu-Abied M, Sadot E, Yalovsky S. Ectopic expression of an activated RAC in Arabidopsis disrupts membrane cycling. Mol Biol Cell 2005; 16:1913-27. [PMID: 15703216 PMCID: PMC1073671 DOI: 10.1091/mbc.e04-07-0562] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Rho GTPases regulate the actin cytoskeleton, exocytosis, endocytosis, and other signaling cascades. Rhos are subdivided into four subfamilies designated Rho, Racs, Cdc42, and a plant-specific group designated RACs/Rops. This research demonstrates that ectopic expression of a constitutive active Arabidopsis RAC, AtRAC10, disrupts actin cytoskeleton organization and membrane cycling. We created transgenic plants expressing either wild-type or constitutive active AtRAC10 fused to the green fluorescent protein. The activated AtRAC10 induced deformation of root hairs and leaf epidermal cells and was primarily localized in Triton X-100-insoluble fractions of the plasma membrane. Actin cytoskeleton reorganization was revealed by creating double transgenic plants expressing activated AtRAC10 and the actin marker YFP-Talin. Plants were further analyzed by membrane staining with N-[3-triethylammoniumpropyl]-4-[p-diethylaminophenylhexatrienyl] pyridinium dibromide (FM4-64) under different treatments, including the protein trafficking inhibitor brefeldin A or the actin-depolymeryzing agents latrunculin-B (Lat-B) and cytochalasin-D (CD). After drug treatments, activated AtRAC10 did not accumulate in brefeldin A compartments, but rather reduced their number and colocalized with FM4-64-labeled membranes in large intracellular vesicles. Furthermore, endocytosis was compromised in root hairs of activated AtRAC10 transgenic plants. FM4-64 was endocytosed in nontransgenic root hairs treated with the actin-stabilizing drug jasplakinolide. These findings suggest complex regulation of membrane cycling by plant RACs.
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Affiliation(s)
- Daria Bloch
- Department of Plant Sciences, Tel Aviv University, Israel
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