1
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Henry AR, Miller ND, Spalding EP. QTL for the Kinematic Traits That Define the Arabidopsis Root Elongation Zone and Their Relationship to Gravitropism. PLANTS (BASEL, SWITZERLAND) 2024; 13:1189. [PMID: 38732404 PMCID: PMC11085590 DOI: 10.3390/plants13091189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell expansion in a discrete region called the elongation zone drives root elongation. Analyzing time lapse images can quantify the expansion in kinematic terms as if it were fluid flow. We used horizontal microscopes to collect images from which custom software extracted the length of the elongation zone, the peak relative elemental growth rate (REGR) within it, the axial position of the REGR peak, and the root elongation rate. Automation enabled these kinematic traits to be measured in 1575 Arabidopsis seedlings representing 162 recombinant inbred lines (RILs) derived from a cross of Cvi and Ler ecotypes. We mapped ten quantitative trait loci (QTL), affecting the four kinematic traits. Three QTL affected two or more traits in these vertically oriented seedlings. We compared this genetic architecture with that previously determined for gravitropism using the same RIL population. The major QTL peaks for the kinematic traits did not overlap with the gravitropism QTL. Furthermore, no single kinematic trait correlated with quantitative descriptors of the gravitropism response curve across this population. In addition to mapping QTL for growth zone traits, this study showed that the size and shape of the elongation zone may vary widely without affecting the differential growth induced by gravity.
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Affiliation(s)
| | | | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA; (A.R.H.); (N.D.M.)
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2
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Ercoli MF, Shigenaga AM, de Araujo AT, Jain R, Ronald PC. Tyrosine-sulfated peptide hormone induces flavonol biosynthesis to control elongation and differentiation in Arabidopsis primary root. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578681. [PMID: 38352507 PMCID: PMC10862922 DOI: 10.1101/2024.02.02.578681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
In Arabidopsis roots, growth initiation and cessation are organized into distinct zones. How regulatory mechanisms are integrated to coordinate these processes and maintain proper growth progression over time is not well understood. Here, we demonstrate that the peptide hormone PLANT PEPTIDE CONTAINING SULFATED TYROSINE 1 (PSY1) promotes root growth by controlling cell elongation. Higher levels of PSY1 lead to longer differentiated cells with a shootward displacement of characteristics common to mature cells. PSY1 activates genes involved in the biosynthesis of flavonols, a group of plant-specific secondary metabolites. Using genetic and chemical approaches, we show that flavonols are required for PSY1 function. Flavonol accumulation downstream of PSY1 occurs in the differentiation zone, where PSY1 also reduces auxin and reactive oxygen species (ROS) activity. These findings support a model where PSY1 signals the developmental-specific accumulation of secondary metabolites to regulate the extent of cell elongation and the overall progression to maturation.
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Affiliation(s)
- Maria Florencia Ercoli
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley 94720
| | - Alexandra M Shigenaga
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Artur Teixeira de Araujo
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Joint Bioenergy Institute, Emeryville, California
| | - Rashmi Jain
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley 94720
- The Joint Bioenergy Institute, Emeryville, California
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3
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Kumar V, Wegener M, Knieper M, Kaya A, Viehhauser A, Dietz KJ. Strategies of Molecular Signal Integration for Optimized Plant Acclimation to Stress Combinations. Methods Mol Biol 2024; 2832:3-29. [PMID: 38869784 DOI: 10.1007/978-1-0716-3973-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Plant growth and survival in their natural environment require versatile mitigation of diverse threats. The task is especially challenging due to the largely unpredictable interaction of countless abiotic and biotic factors. To resist an unfavorable environment, plants have evolved diverse sensing, signaling, and adaptive molecular mechanisms. Recent stress studies have identified molecular elements like secondary messengers (ROS, Ca2+, etc.), hormones (ABA, JA, etc.), and signaling proteins (SnRK, MAPK, etc.). However, major gaps remain in understanding the interaction between these pathways, and in particular under conditions of stress combinations. Here, we highlight the challenge of defining "stress" in such complex natural scenarios. Therefore, defining stress hallmarks for different combinations is crucial. We discuss three examples of robust and dynamic plant acclimation systems, outlining specific plant responses to complex stress overlaps. (a) The high plasticity of root system architecture is a decisive feature in sustainable crop development in times of global climate change. (b) Similarly, broad sensory abilities and apparent control of cellular metabolism under adverse conditions through retrograde signaling make chloroplasts an ideal hub. Functional specificity of the chloroplast-associated molecular patterns (ChAMPs) under combined stresses needs further focus. (c) The molecular integration of several hormonal signaling pathways, which bring together all cellular information to initiate the adaptive changes, needs resolving.
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Affiliation(s)
- Vijay Kumar
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Melanie Wegener
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Madita Knieper
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Armağan Kaya
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Andrea Viehhauser
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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4
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Goh T, Song Y, Yonekura T, Obushi N, Den Z, Imizu K, Tomizawa Y, Kondo Y, Miyashima S, Iwamoto Y, Inami M, Chen YW, Nakajima K. In-Depth Quantification of Cell Division and Elongation Dynamics at the Tip of Growing Arabidopsis Roots Using 4D Microscopy, AI-Assisted Image Processing and Data Sonification. PLANT & CELL PHYSIOLOGY 2023; 64:1262-1278. [PMID: 37861079 DOI: 10.1093/pcp/pcad105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/21/2023]
Abstract
One of the fundamental questions in plant developmental biology is how cell proliferation and cell expansion coordinately determine organ growth and morphology. An amenable system to address this question is the Arabidopsis root tip, where cell proliferation and elongation occur in spatially separated domains, and cell morphologies can easily be observed using a confocal microscope. While past studies revealed numerous elements of root growth regulation including gene regulatory networks, hormone transport and signaling, cell mechanics and environmental perception, how cells divide and elongate under possible constraints from cell lineages and neighboring cell files has not been analyzed quantitatively. This is mainly due to the technical difficulties in capturing cell division and elongation dynamics at the tip of growing roots, as well as an extremely labor-intensive task of tracing the lineages of frequently dividing cells. Here, we developed a motion-tracking confocal microscope and an Artificial Intelligence (AI)-assisted image-processing pipeline that enables semi-automated quantification of cell division and elongation dynamics at the tip of vertically growing Arabidopsis roots. We also implemented a data sonification tool that facilitates human recognition of cell division synchrony. Using these tools, we revealed previously unnoted lineage-constrained dynamics of cell division and elongation, and their contribution to the root zonation boundaries.
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Affiliation(s)
| | - Yu Song
- College of Information Science and Engineering, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577 Japan
| | - Takaaki Yonekura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033 Japan
| | - Noriyasu Obushi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, 153-8904 Japan
| | - Zeping Den
- College of Information Science and Engineering, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577 Japan
| | - Katsutoshi Imizu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan
| | - Yoko Tomizawa
- The Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787 Japan
| | - Yohei Kondo
- The Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787 Japan
| | - Shunsuke Miyashima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan
| | - Yutaro Iwamoto
- College of Information Science and Engineering, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577 Japan
- Faculty of Information and Communication Engineering, Osaka Electro-Communication University, 18-8 Hatsucho, Neyagawa, Osaka, 572-8530 Japan
| | - Masahiko Inami
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, 153-8904 Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan
| | - Yen-Wei Chen
- College of Information Science and Engineering, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577 Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan
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5
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Lasok H, Nziengui H, Kochersperger P, Ditengou FA. Arabidopsis Root Development Regulation by the Endogenous Folate Precursor, Para-Aminobenzoic Acid, via Modulation of the Root Cell Cycle. PLANTS (BASEL, SWITZERLAND) 2023; 12:4076. [PMID: 38140403 PMCID: PMC10748309 DOI: 10.3390/plants12244076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/15/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023]
Abstract
The continuous growth of roots depends on their ability to maintain a balanced ratio between cell production and cell differentiation at the tip. This process is regulated by the hormonal balance of cytokinin and auxin. However, other important regulators, such as plant folates, also play a regulatory role. In this study, we investigated the impact of the folate precursor para-aminobenzoic acid (PABA) on root development. Using pharmacological, genetic, and imaging approaches, we show that the growth of Arabidopsis thaliana roots is repressed by either supplementing the growth medium with PABA or overexpressing the PABA synthesis gene GAT-ADCS. This is associated with a smaller root meristem consisting of fewer cells. Conversely, reducing the levels of free root endogenous PABA results in longer roots with extended meristems. We provide evidence that PABA represses Arabidopsis root growth in a folate-independent manner and likely acts through two mechanisms: (i) the G2/M transition of cell division in the root apical meristem and (ii) promoting premature cell differentiation in the transition zone. These data collectively suggest that PABA plays a role in Arabidopsis root growth at the intersection between cell division and cell differentiation.
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Affiliation(s)
- Hanna Lasok
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Kraków, Poland;
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Hugues Nziengui
- Department of Biology, Faculty of Sciences, Science and Technology University of Masuku, Franceville P.O. Box 913, Gabon;
| | - Philip Kochersperger
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Franck Anicet Ditengou
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany
- Lighthouse Core Facility, Medical Center University of Freiburg, Albert Ludwigs University Freiburg, 79106 Freiburg, Germany
- Bio Imaging Core Light Microscopy (BiMiC), Institute for Disease Modelling and Targeted Medicine (IMITATE), Medical Center University of Freiburg, Albert Ludwigs University Freiburg, 79106 Freiburg, Germany
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6
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Nolan TM, Shahan R. Resolving plant development in space and time with single-cell genomics. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102444. [PMID: 37696725 DOI: 10.1016/j.pbi.2023.102444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Single-cell genomics technologies are ushering in a new research era. In this review, we summarize the benefits and current challenges of using these technologies to probe the transcriptional regulation of plant development. In addition to profiling cells at a single snapshot in time, researchers have recently produced time-resolved datasets to map cell responses to stimuli. Live-imaging and spatial transcriptomic techniques are rapidly being adopted to link a cell's transcriptional profile with its spatial location within a tissue. Combining these technologies is a powerful spatiotemporal approach to investigate cell plasticity and developmental responses that contribute to plant resilience. Although there are hurdles to overcome, we conclude by discussing how single-cell genomics is poised to address developmental questions in the coming years.
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Affiliation(s)
- Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
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7
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Henry AR, Miller ND, Spalding EP. Patch Track Software for Measuring Kinematic Phenotypes of Arabidopsis Roots Demonstrated on Auxin Transport Mutants. Int J Mol Sci 2023; 24:16475. [PMID: 38003665 PMCID: PMC10671601 DOI: 10.3390/ijms242216475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Plant roots elongate when cells produced in the apical meristem enter a transient period of rapid expansion. To measure the dynamic process of root cell expansion in the elongation zone, we captured digital images of growing Arabidopsis roots with horizontal microscopes and analyzed them with a custom image analysis program (PatchTrack) designed to track the growth-driven displacement of many closely spaced image patches. Fitting a flexible logistics equation to patch velocities plotted versus position along the root axis produced the length of the elongation zone (mm), peak relative elemental growth rate (% h-1), the axial position of the peak (mm from the tip), and average root elongation rate (mm h-1). For a wild-type root, the average values of these kinematic traits were 0.52 mm, 23.7% h-1, 0.35 mm, and 0.1 mm h-1, respectively. We used the platform to determine the kinematic phenotypes of auxin transport mutants. The results support a model in which the PIN2 auxin transporter creates an area of expansion-suppressing, supraoptimal auxin concentration that ends 0.1 mm from the quiescent center (QC), and that ABCB4 and ABCB19 auxin transporters maintain expansion-limiting suboptimal auxin levels beginning approximately 0.5 mm from the QC. This study shows that PatchTrack can quantify dynamic root phenotypes in kinematic terms.
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Affiliation(s)
| | | | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA (N.D.M.)
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8
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Mira MM, El-Khateeb EA, Youssef MS, Ciacka K, So K, Duncan RW, Hill RD, Stasolla C. Arabidopsis root apical meristem survival during waterlogging is determined by phytoglobin through nitric oxide and auxin. PLANTA 2023; 258:86. [PMID: 37747517 DOI: 10.1007/s00425-023-04239-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
MAIN CONCLUSION Over-expression of phytoglobin mitigates the degradation of the root apical meristem (RAM) caused by waterlogging through changes in nitric oxide and auxin distribution at the root tip. Plant performance to waterlogging is ameliorated by the over-expression of the Arabidopsis Phytoglobin 1 (Pgb1) which also contributes to the maintenance of a functional RAM. Hypoxia induces accumulation of ROS and damage in roots of wild type plants; these events were preceded by the exhaustion of the RAM resulting from the loss of functionality of the WOX5-expressing quiescent cells (QCs). These phenotypic deviations were exacerbated by suppression of Pgb1 and attenuated when the same gene was up-regulated. Genetic and pharmacological studies demonstrated that degradation of the RAM in hypoxic roots is attributed to a reduction in the auxin maximum at the root tip, necessary for the specification of the QC. This reduction was primarily caused by alterations in PIN-mediated auxin flow but not auxin synthesis. The expression and localization patterns of several PINs, including PIN1, 2, 3 and 4, facilitating the basipetal translocation of auxin and its distribution at the root tip, were altered in hypoxic WT and Pgb1-suppressing roots but mostly unchanged in those over-expressing Pgb1. Disruption of PIN1 and PIN2 signal in hypoxic roots suppressing Pgb1 initiated in the transition zone at 12 h and was specifically associated to the absence of Pgb1 protein in the same region. Exogenous auxin restored a functional RAM, while inhibition of the directional auxin flow exacerbated the degradation of the RAM. The regulation of root behavior by Pgb1 was mediated by nitric oxide (NO) in a model consistent with the recognized function of Pgbs as NO scavengers. Collectively, this study contributes to our understanding of the role of Pgbs in preserving root meristem function and QC niche during conditions of stress, and suggests that the root transition zone is most vulnerable to hypoxia.
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Affiliation(s)
- Mohammed M Mira
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Eman A El-Khateeb
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed S Youssef
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Botany and Microbiology, Faculty of Science, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - Katarzyna Ciacka
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Kenny So
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Robert W Duncan
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Robert D Hill
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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9
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Del Dottore E, Mazzolai B. Perspectives on Computation in Plants. ARTIFICIAL LIFE 2023; 29:336-350. [PMID: 36787453 DOI: 10.1162/artl_a_00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Plants thrive in virtually all natural and human-adapted environments and are becoming popular models for developing robotics systems because of their strategies of morphological and behavioral adaptation. Such adaptation and high plasticity offer new approaches for designing, modeling, and controlling artificial systems acting in unstructured scenarios. At the same time, the development of artifacts based on their working principles reveals how plants promote innovative approaches for preservation and management plans and opens new applications for engineering-driven plant science. Environmentally mediated growth patterns (e.g., tropisms) are clear examples of adaptive behaviors displayed through morphological phenotyping. Plants also create networks with other plants through subterranean roots-fungi symbiosis and use these networks to exchange resources or warning signals. This article discusses the functional behaviors of plants and shows the close similarities with a perceptron-like model that could act as a behavior-based control model in plants. We begin by analyzing communication rules and growth behaviors of plants; we then show how we translated plant behaviors into algorithmic solutions for bioinspired robot controllers; and finally, we discuss how those solutions can be extended to embrace original approaches to networking and robotics control architectures.
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Affiliation(s)
| | - Barbara Mazzolai
- Bioinspired Soft Robotics Laboratory, Istituto Italiano di Tecnologia.
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10
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Kikuchi S, Sakamoto T, Matsunaga S, Iwamoto A. Novel whole-mount FISH analysis for intact root of Arabidopsis thaliana with spatial reference to 3D visualization. JOURNAL OF PLANT RESEARCH 2023; 136:423-428. [PMID: 36719512 DOI: 10.1007/s10265-023-01438-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Whole-mount fluorescent in situ hybridization (WM-FISH) is an effective tool to observe chromosome behavior in tissues or organs. However, it is difficult to obtain a precise spatial profile of fluorescent signals in roots using conventional WM-FISH mainly because of the severe damage caused during the processing. To address this problem, we established a novel WM-FISH analysis for intact roots of Arabidopsis thaliana and successfully obtained a precise spatial profile of nuclear size and centromere signals. The two main improvements in the novel WM-FISH analysis are: (i) hybridization was performed directly on MAS-coated glass slides covered with silicon wells and (ii) conditions for enzyme treatment were optimized (37 °C, 45 s). After the WM-FISH using a centromere probe, we analyzed the results by 3D data processing to quantify the nuclear volume and number of centromere signals of the obtained cortical cell files and determined the position of each nucleus in intact roots. Then we plotted the nuclear volume and number of centromere signals versus distance from the quiescent center to evaluate the precise spatial profile of each parameter.
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Affiliation(s)
- Suzuka Kikuchi
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, 2946, 259-1293, Tsuchiya, Hiratsuka, Kanagawa, Japan.
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, 278-8510, Noda, Chiba, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, 277-8561, Kashiwa, Chiba, Japan
| | - Akitoshi Iwamoto
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, 2946, 259-1293, Tsuchiya, Hiratsuka, Kanagawa, Japan
- Department of Biological Science, Faculty of Science, Kanagawa University, 2946, 259-1293, Tsuchiya, Hiratsuka, Kanagawa, Japan
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11
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Nolan TM, Vukašinović N, Hsu CW, Zhang J, Vanhoutte I, Shahan R, Taylor IW, Greenstreet L, Heitz M, Afanassiev A, Wang P, Szekely P, Brosnan A, Yin Y, Schiebinger G, Ohler U, Russinova E, Benfey PN. Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. Science 2023; 379:eadf4721. [PMID: 36996230 PMCID: PMC10119888 DOI: 10.1126/science.adf4721] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 04/01/2023]
Abstract
Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and cell elongation, through gene regulatory networks that vary in space and time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive gene expression specific to different cell types and developmental stages of the Arabidopsis root, we identified the elongating cortex as a site where brassinosteroids trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed HOMEOBOX FROM ARABIDOPSIS THALIANA 7 (HAT7) and GT-2-LIKE 1 (GTL1) as brassinosteroid-responsive transcription factors that regulate cortex cell elongation. These results establish the cortex as a site of brassinosteroid-mediated growth and unveil a brassinosteroid signaling network regulating the transition from proliferation to elongation, which illuminates aspects of spatiotemporal hormone responses.
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Affiliation(s)
| | - Nemanja Vukašinović
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Che-Wei Hsu
- Department of Biology, Duke University, Durham, NC, USA
- Department of Biology, Humboldt Universitat zu Berlin, Berlin, Germany
- The Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | | | - Isabelle Vanhoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | | | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Matthieu Heitz
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Ping Wang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Pablo Szekely
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Aiden Brosnan
- Department of Biology, Duke University, Durham, NC, USA
| | - Yanhai Yin
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Uwe Ohler
- Department of Biology, Humboldt Universitat zu Berlin, Berlin, Germany
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
- Department of Computer Science, Humboldt Universitat zu Berlin, Berlin, Germany
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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12
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Shtin M, Polverari L, Svolacchia N, Bertolotti G, Unterholzner SJ, Di Mambro R, Costantino P, Dello Ioio R, Sabatini S. The Mutual Inhibition between PLETHORAs and ARABIDOPSIS RESPONSE REGULATORs Controls Root Zonation. PLANT & CELL PHYSIOLOGY 2023; 64:317-324. [PMID: 36611272 DOI: 10.1093/pcp/pcad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/10/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
During organogenesis, a key step toward the development of a functional organ is the separation of cells into specific domains with different activities. Mutual inhibition of gene expression has been shown to be sufficient to establish and maintain these domains during organogenesis in several multicellular organisms. Here, we show that the mutual inhibition between the PLETHORA transcription factors (PLTs) and the ARABIDOPSIS RESPONSE REGULATORs (ARRs) transcription factors is sufficient to separate cell division and cell differentiation during root organogenesis. In particular, we show that ARR1 suppresses PLT activities and that PLTs suppress ARR1 and ARR12 by targeting their proteins for degradation via the KISS ME DEADLY 2 F-box protein. These findings reveal new important aspects of the complex process of root zonation and development.
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Affiliation(s)
- Margaryta Shtin
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazzale Università 5, Bolzano 39100, Italy
| | - Laura Polverari
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Noemi Svolacchia
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Gaia Bertolotti
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Simon J Unterholzner
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazzale Università 5, Bolzano 39100, Italy
| | - Riccardo Di Mambro
- Department of Biology, University of Pisa, via L. Ghini, 13, Pisa 56126, Italy
| | - Paolo Costantino
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
| | - Raffaele Dello Ioio
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
- Department of Biology, University of Pisa, via L. Ghini, 13, Pisa 56126, Italy
| | - Sabrina Sabatini
- Department of Biology and Biotechnology 'Charles Darwin', University of Rome 'Sapienza', via dei Sardi 70, Rome 00185, Italy
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13
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Friero I, Larriba E, Martínez-Melgarejo PA, Justamante MS, Alarcón MV, Albacete A, Salguero J, Pérez-Pérez JM. Transcriptomic and hormonal analysis of the roots of maize seedlings grown hydroponically at low temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111525. [PMID: 36328179 DOI: 10.1016/j.plantsci.2022.111525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/23/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Prolonged cold stress has a strong effect on plant growth and development, especially in subtropical crops such as maize. Soil temperature limits primary root elongation, mainly during early seedling establishment. However, little is known about how moderate temperature fluctuations affect root growth at the molecular and physiological levels. We have studied root tips of young maize seedlings grown hydroponically at 30 ºC and after a short period (up to 24 h) of moderate cooling (20 ºC). We found that both cell division and cell elongation in the root apical meristem are affected by temperature. Time-course analyses of hormonal and transcriptomic profiles were achieved after temperature reduction from 30 ºC to 20 ºC. Our results highlighted a complex regulation of endogenous pathways leading to adaptive root responses to moderate cooling conditions.
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Affiliation(s)
- Iván Friero
- Departamento de Biología Vegetal, Ecología y Ciencias de la Tierra, Universidad de Extremadura, 06006 Badajoz, Spain.
| | - Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain.
| | | | | | - M Victoria Alarcón
- Área de Agronomía de Cultivos Leñosos y Hortícolas, Instituto de Investigaciones Agrarias "La Orden-Valdesequera" (CICYTEX), Junta de Extremadura, 06187 Badajoz, Spain.
| | - Alfonso Albacete
- Departamento de Nutrición Vegetal, CEBAS-CSIC, 30100 Murcia, Spain.
| | - Julio Salguero
- Departamento de Biología Vegetal, Ecología y Ciencias de la Tierra, Universidad de Extremadura, 06006 Badajoz, Spain.
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14
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Poulios S, Tsilimigka F, Mallioura A, Pappas D, Seira E, Vlachonasios K. Histone Acetyltransferase GCN5 Affects Auxin Transport during Root Growth by Modulating Histone Acetylation and Gene Expression of PINs. PLANTS (BASEL, SWITZERLAND) 2022; 11:3572. [PMID: 36559684 PMCID: PMC9781282 DOI: 10.3390/plants11243572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
General Control Non-Derepressible 5 (GCN5) is a histone acetyltransferase that targets multiple genes and is essential for the acetylation of Lysine residues in the N-terminal tail of histone H3 in Arabidopsis. GCN5 interacts with the transcriptional coactivator Alteration/Deficiency in Activation 2b (ADA2b), which enhances its activity functioning in multiprotein complexes, such as the Spt-Ada-Gcn5-Acetyltransferase complex (SAGA). Mutations in GCN5 and ADA2b result in pleiotropic phenotypes, including alterations in the growth of roots. Auxin is known to regulate root development by modulating gene expression patterns. Auxin moves polarly during plant growth via the Pin-formed (PIN) auxin efflux transport proteins. The effect of GCN5 and ADA2b on auxin distribution at different stages of early root growth (4 to 7 days post-germination) was studied using the reporter lines DR5rev::GFP and PIN1::PIN1-GFP. In wild-type plants, auxin efflux transporter PIN1 expression increases from the fourth to the seventh day of root growth. The PIN1 expression was reduced in the roots of gcn5-1 and ada2b-1 compared to the wild type. The expression of PIN1 in ada2b-1 mutants is confined only to the meristematic zone, specifically in the stele cells, whereas it is almost abolished in the elongation zone. Gene expression analysis showed that genes associated with auxin transport, PIN1, PIN3 and PIN4, are downregulated in gcn5-1 and ada2b-1 mutants relative to the wild type. As a result, auxin accumulation was also reduced in gcn5-1 and ada2b-1 compared to wild-type roots. Furthermore, acetylation of Lysine 14 of histone H3 (H3K14) was also affected in the promoter and coding region of PIN1, PIN3 and PIN4 genes during root growth of Arabidopsis in gcn5 mutants. In conclusion, GCN5 acts as a positive regulator of auxin distribution in early root growth by modulating histone H3 acetylation and the expression of auxin efflux transport genes.
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Affiliation(s)
- Stylianos Poulios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Foteini Tsilimigka
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Postgraduate Program Studies “Applications of Biology—Biotechnology, Molecular and Microbial Analysis of Food and Products”, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Areti Mallioura
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Postgraduate Program Studies “Applications of Biology—Biotechnology, Molecular and Microbial Analysis of Food and Products”, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitris Pappas
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Eleftheria Seira
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Postgraduate Program Studies “Applications of Biology—Biotechnology, Molecular and Microbial Analysis of Food and Products”, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Konstantinos Vlachonasios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Natural Products Research Centre of Excellence (NatPro-AUTh), Center of Interdisciplinary Research and Innovation of Aristotle University of Thessaloniki (CIRI-AUTh), 57001 Thessaloniki, Greece
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15
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Üstüner S, Schäfer P, Eichmann R. Development specifies, diversifies and empowers root immunity. EMBO Rep 2022; 23:e55631. [PMID: 36330761 PMCID: PMC9724680 DOI: 10.15252/embr.202255631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 08/04/2023] Open
Abstract
Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.
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Affiliation(s)
- Sim Üstüner
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
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16
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García-Gómez ML, Reyes-Hernández BJ, Sahoo DP, Napsucialy-Mendivil S, Quintana-Armas AX, Pedroza-García JA, Shishkova S, Torres-Martínez HH, Pacheco-Escobedo MA, Dubrovsky JG. A mutation in THREONINE SYNTHASE 1 uncouples proliferation and transition domains of the root apical meristem: experimental evidence and in silico proposed mechanism. Development 2022; 149:278438. [PMID: 36278862 PMCID: PMC9796171 DOI: 10.1242/dev.200899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022]
Abstract
A continuum from stem to transit-amplifying to a differentiated cell state is a common theme in multicellular organisms. In the plant root apical meristem (RAM), transit-amplifying cells are organized into two domains: cells from the proliferation domain (PD) are displaced to the transition domain (TD), suggesting that both domains are necessarily coupled. Here, we show that in the Arabidopsis thaliana mto2-2 mutant, in which threonine (Thr) synthesis is affected, the RAM lacks the PD. Through a combination of cell length profile analysis, mathematical modeling and molecular markers, we establish that the PD and TD can be uncoupled. Remarkably, although the RAM of mto2-2 is represented solely by the TD, the known factors of RAM maintenance and auxin signaling are expressed in the mutant. Mathematical modeling predicts that the stem cell niche depends on Thr metabolism and that, when disturbed, the normal continuum of cell states becomes aborted.
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Affiliation(s)
- Monica L. García-Gómez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Blanca J. Reyes-Hernández
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Debee P. Sahoo
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Aranza X. Quintana-Armas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - José A. Pedroza-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Svetlana Shishkova
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Héctor H. Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Mario A. Pacheco-Escobedo
- Facultad de Ciencias de la Salud, Universidad Tecnológica de México – UNITEC MÉXICO – Campus Atizapán, Av. Calacoaya 7, Atizapán de Zaragoza, Estado de México, 52970, Mexico
| | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico,Author for correspondence ()
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17
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He Q, Yuan R, Zhang T, An F, Wang N, Lan J, Wang X, Zhang Z, Pan Y, Wang X, Zhang J, Guo D, Qin G. Arabidopsis TIE1 and TIE2 transcriptional repressors dampen cytokinin response during root development. SCIENCE ADVANCES 2022; 8:eabn5057. [PMID: 36083905 PMCID: PMC9462699 DOI: 10.1126/sciadv.abn5057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Cytokinin plays critical roles in root development. Cytokinin signaling depends on activation of key transcription factors known as type B Arabidopsis response regulators (ARRs). However, the mechanisms underlying the finely tuned regulation of type B ARR activity remain unclear. In this study, we demonstrate that the ERF-associated amphiphilic repression (EAR) motif-containing protein TCP interactor containing ear motif protein2 (TIE2) forms a negative feedback loop to finely tune the activity of type B ARRs during root development. Disruption of TIE2 and its close homolog TIE1 causes severely shortened roots. TIE2 interacts with type B ARR1 and represses transcription of ARR1 targets. The cytokinin response is correspondingly enhanced in tie1-1 tie2-1. We further show that ARR1 positively regulates TIE1 and TIE2 by directly binding to their promoters. Our findings demonstrate that TIEs play key roles in controlling plant development and reveal an important negative feedback regulation mechanism for cytokinin signaling.
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18
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Wang M, Danz K, Ly V, Rojas-Pierce M. Microgravity enhances the phenotype of Arabidopsis zigzag-1 and reduces the Wortmannin-induced vacuole fusion in root cells. NPJ Microgravity 2022; 8:38. [PMID: 36064795 PMCID: PMC9445043 DOI: 10.1038/s41526-022-00226-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/23/2022] [Indexed: 12/04/2022] Open
Abstract
The spaceflight environment of the International Space Station poses a multitude of stresses on plant growth including reduced gravity. Plants exposed to microgravity and other conditions on the ISS display root skewing, changes in gene expression and protein abundance that may result in changes in cell wall composition, antioxidant accumulation and modification of growth anisotropy. Systematic studies that address the effects of microgravity on cellular organelles are lacking but altered numbers and sizes of vacuoles have been detected in previous flights. The prominent size of plant vacuoles makes them ideal models to study organelle dynamics in space. Here, we used Arabidopsiszigzag-1 (zig-1) as a sensitized genotype to study the effect of microgravity on plant vacuole fusion. Wortmannin was used to induce vacuole fusion in seedlings and a formaldehyde-based fixation protocol was developed to visualize plant vacuole morphology after sample return, using confocal microscopy. Our results indicate that microgravity enhances the zig-1 phenotype by reducing hypocotyl growth and vacuole fusion in some cells. This study demonstrates the feasibility of chemical inhibitor treatments for plant cell biology experiments in space.
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Affiliation(s)
- Mengying Wang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Katherine Danz
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Vanessa Ly
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Marcela Rojas-Pierce
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
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19
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ADA2b and GCN5 Affect Cytokinin Signaling by Modulating Histone Acetylation and Gene Expression during Root Growth of Arabidopsis thaliana. PLANTS 2022; 11:plants11101335. [PMID: 35631760 PMCID: PMC9148027 DOI: 10.3390/plants11101335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
Abstract
In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. The early root growth (4 to 7 days post-germination) was analyzed using cellular and molecular approaches. TCS signal accumulated from the fourth to seventh days of root growth in the wild-type columella cells. In contrast, ada2b-1 and gcn5-1 and ada2a-2ada2b-1 double mutants displayed reduced TCS expression relative to wild type. Gene expression analysis showed that genes associated with cytokinin homeostasis were downregulated in the roots of gcn5-1 and ada2b-1 mutants compared to wild-type plants. H3K14 acetylation was affected in the promoters of cytokinin synthesis and catabolism genes during root growth of Arabidopsis. Therefore, GCN5 and ADA2b are positive regulators of cytokinin signaling during root growth by modulating histone acetylation and the expression of genes involved in cytokinin synthesis and catabolism. Auxin application in the roots of wild-type seedlings increased TCS::GFP expression. In contrast, ada2b and ada2ada2b mutant plants do not show the auxin-induced TCS signal, suggesting that GCN5 and ADA2b are required for the auxin-induced cytokinin signaling in early root growth.
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20
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Liu S, Strauss S, Adibi M, Mosca G, Yoshida S, Dello Ioio R, Runions A, Andersen TG, Grossmann G, Huijser P, Smith RS, Tsiantis M. Cytokinin promotes growth cessation in the Arabidopsis root. Curr Biol 2022; 32:1974-1985.e3. [PMID: 35354067 DOI: 10.1016/j.cub.2022.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/21/2021] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
Abstract
The Arabidopsis root offers good opportunities to investigate how regulated cellular growth shapes different tissues and organs, a key question in developmental biology. Along the root's longitudinal axis, cells sequentially occupy different developmental states. Proliferative meristematic cells give rise to differentiating cells, which rapidly elongate in the elongation zone, then mature and stop growing in the differentiation zone. The phytohormone cytokinin contributes to this zonation by positioning the boundary between the meristem and the elongation zone, called the transition zone. However, the cellular growth profile underlying root zonation is not well understood, and the cellular mechanisms that mediate growth cessation remain unclear. By using time-lapse imaging, genetics, and computational analysis, we analyze the effect of cytokinin on root zonation and cellular growth. We found that cytokinin promotes growth cessation in the distal (shootward) elongation zone in conjunction with accelerating the transition from elongation to differentiation. We estimated cell-wall stiffness by using osmotic treatment experiments and found that cytokinin-mediated growth cessation is associated with cell-wall stiffening and requires the action of an auxin influx carrier, AUX1. Our measurement of growth and cell-wall mechanical properties at a cellular resolution reveal mechanisms via which cytokinin influences cell behavior to shape tissue patterns.
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Affiliation(s)
- Shanda Liu
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Milad Adibi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Gabriella Mosca
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany; Physics Department, Technical University Munich, James-Franck-Str. 1/I, 85748 Garching b. Munich, Germany
| | - Saiko Yoshida
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza, via dei Sardi, 70, 00185 Rome, Italy
| | - Adam Runions
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Tonni Grube Andersen
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Guido Grossmann
- Institute for Cell and Interaction Biology, Heinrich-Heine Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany; Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany.
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21
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Shtin M, Dello Ioio R, Del Bianco M. It's Time for a Change: The Role of Gibberellin in Root Meristem Development. FRONTIERS IN PLANT SCIENCE 2022; 13:882517. [PMID: 35592570 PMCID: PMC9112047 DOI: 10.3389/fpls.2022.882517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/14/2022] [Indexed: 05/21/2023]
Abstract
One of the most amazing characteristics of plants is their ability to grow and adapt their development to environmental changes. This fascinating feature is possible thanks to the activity of meristems, tissues that contain lasting self-renewal stem cells. Because of its simple and symmetric structure, the root meristem emerged as a potent system to uncover the developmental mechanisms behind the development of the meristems. The root meristem is formed during embryogenesis and sustains root growth for all the plant's lifetime. In the last decade, gibberellins have emerged as a key regulator for root meristem development. This phytohormone functions as a molecular clock for root development. This mini review discusses the latest advances in understanding the role of gibberellin in root development and highlights the central role of this hormone as developmental timer.
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Affiliation(s)
- Margaryta Shtin
- Department of Biology and Biotechnology “C. Darwin”, Laboratory of Functional Genomics and Proteomics of Model Systems, University of Rome “Sapienza”, Rome, Italy
| | - Raffaele Dello Ioio
- Department of Biology and Biotechnology “C. Darwin”, Laboratory of Functional Genomics and Proteomics of Model Systems, University of Rome “Sapienza”, Rome, Italy
- *Correspondence: Raffaele Dello Ioio,
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22
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Pasternak T, Pérez-Pérez JM. Methods of In Situ Quantitative Root Biology. PLANTS (BASEL, SWITZERLAND) 2021; 10:2399. [PMID: 34834762 PMCID: PMC8625443 DOI: 10.3390/plants10112399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022]
Abstract
When dealing with plant roots, a multiscale description of the functional root structure is needed. Since the beginning of 21st century, new devices such as laser confocal microscopes have been accessible for coarse root structure measurements, including three-dimensional (3D) reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitative determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for 3D analysis of root features at single-cell resolution, including root asymmetry, lateral root analysis, cell size and nuclear organization, cell-cycle kinetics, and chromatin structure analysis. Quantitative maps of the root apical meristem (RAM) are shown for different species, including Arabidopsis thaliana (L.), Heynh, Nicotiana tabacum L., Medicago sativa L., and Setaria italica (L.) P. Beauv. The 3D analysis of the RAM in these species showed divergence in chromatin organization and cell volume distribution that might be used to study root zonation for each root tissue. Detailed protocols and possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.
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Affiliation(s)
- Taras Pasternak
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Institute of Biology II/Molecular Plant Physiology, 79104 Freiburg, Germany
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Bertolotti G, Scintu D, Dello Ioio R. A small cog in a large wheel: crucial role of miRNAs in root apical meristem patterning. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6755-6767. [PMID: 34350947 DOI: 10.1093/jxb/erab332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
In both animal and plants, establishment of body axes is fundamental for proper organ development. Plant roots show two main developmental axes: the proximo-distal axis, which spans from the hypocotyl-root junction to the root tip; and the radial axis, which traverses from the vascular tissue to the epidermis. Root axes are determined in the root meristem. The root meristem occupies the tip of the root and contains self-renewing stem cells, which continuously produce new root cells. An intricate network of signalling pathways regulates meristem function and patterning to ensure proper root development and growth. In the last decade, miRNAs, 20-21 nucleotide-long molecules with morphogenetic activity, emerged as central regulators of root cell patterning. Their activity intersects with master regulators of meristematic activity, including phytohormones. In this review, we discuss the latest findings about the activity of miRNAs and their interaction with other molecular networks in the formation of root meristem axes. Furthermore, we describe how these small molecules allow root growth to adapt to changes in the environment, while maintaining the correct patterning.
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Affiliation(s)
- Gaia Bertolotti
- University of Rome 'La Sapienza', Department of Biology and Biotechnology, 'Charles Darwin', Via dei Sardi 70, Rome, Italy
| | - Daria Scintu
- University of Rome 'La Sapienza', Department of Biology and Biotechnology, 'Charles Darwin', Via dei Sardi 70, Rome, Italy
| | - Raffaele Dello Ioio
- University of Rome 'La Sapienza', Department of Biology and Biotechnology, 'Charles Darwin', Via dei Sardi 70, Rome, Italy
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Yamoune A, Cuyacot AR, Zdarska M, Hejatko J. Hormonal orchestration of root apical meristem formation and maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6768-6788. [PMID: 34343283 DOI: 10.1093/jxb/erab360] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Plant hormones are key regulators of a number of developmental and adaptive responses in plants, integrating the control of intrinsic developmental regulatory circuits with environmental inputs. Here we provide an overview of the molecular mechanisms underlying hormonal regulation of root development. We focus on key events during both embryonic and post-embryonic development, including specification of the hypophysis as a future organizer of the root apical meristem (RAM), hypophysis asymmetric division, specification of the quiescent centre (QC) and the stem cell niche (SCN), RAM maturation and maintenance of QC/SCN activity, and RAM size. We address both well-established and newly proposed concepts, highlight potential ambiguities in recent terminology and classification criteria of longitudinal root zonation, and point to contrasting results and alternative scenarios for recent models. In the concluding remarks, we summarize the common principles of hormonal control during root development and the mechanisms potentially explaining often antagonistic outputs of hormone action, and propose possible future research directions on hormones in the root.
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Affiliation(s)
- Amel Yamoune
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Abigail Rubiato Cuyacot
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Marketa Zdarska
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jan Hejatko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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25
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Mallatt J, Blatt MR, Draguhn A, Robinson DG, Taiz L. Debunking a myth: plant consciousness. PROTOPLASMA 2021; 258:459-476. [PMID: 33196907 PMCID: PMC8052213 DOI: 10.1007/s00709-020-01579-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/22/2020] [Indexed: 05/18/2023]
Abstract
Claims that plants have conscious experiences have increased in recent years and have received wide coverage, from the popular media to scientific journals. Such claims are misleading and have the potential to misdirect funding and governmental policy decisions. After defining basic, primary consciousness, we provide new arguments against 12 core claims made by the proponents of plant consciousness. Three important new conclusions of our study are (1) plants have not been shown to perform the proactive, anticipatory behaviors associated with consciousness, but only to sense and follow stimulus trails reactively; (2) electrophysiological signaling in plants serves immediate physiological functions rather than integrative-information processing as in nervous systems of animals, giving no indication of plant consciousness; (3) the controversial claim of classical Pavlovian learning in plants, even if correct, is irrelevant because this type of learning does not require consciousness. Finally, we present our own hypothesis, based on two logical assumptions, concerning which organisms possess consciousness. Our first assumption is that affective (emotional) consciousness is marked by an advanced capacity for operant learning about rewards and punishments. Our second assumption is that image-based conscious experience is marked by demonstrably mapped representations of the external environment within the body. Certain animals fit both of these criteria, but plants fit neither. We conclude that claims for plant consciousness are highly speculative and lack sound scientific support.
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Affiliation(s)
- Jon Mallatt
- The University of Washington WWAMI Medical Education Program at The University of Idaho, Moscow, ID 83844 USA
| | - Michael R. Blatt
- Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, G12 8QQ UK
| | - Andreas Draguhn
- Institute for Physiology and Pathophysiology, Medical Faculty, University of Heidelberg, 69120 Heidelberg, Germany
| | - David G. Robinson
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Lincoln Taiz
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064 USA
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26
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Mallatt J, Blatt MR, Draguhn A, Robinson DG, Taiz L. Debunking a myth: plant consciousness. PROTOPLASMA 2021. [PMID: 33196907 DOI: 10.1007/s00709-026-01579-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Claims that plants have conscious experiences have increased in recent years and have received wide coverage, from the popular media to scientific journals. Such claims are misleading and have the potential to misdirect funding and governmental policy decisions. After defining basic, primary consciousness, we provide new arguments against 12 core claims made by the proponents of plant consciousness. Three important new conclusions of our study are (1) plants have not been shown to perform the proactive, anticipatory behaviors associated with consciousness, but only to sense and follow stimulus trails reactively; (2) electrophysiological signaling in plants serves immediate physiological functions rather than integrative-information processing as in nervous systems of animals, giving no indication of plant consciousness; (3) the controversial claim of classical Pavlovian learning in plants, even if correct, is irrelevant because this type of learning does not require consciousness. Finally, we present our own hypothesis, based on two logical assumptions, concerning which organisms possess consciousness. Our first assumption is that affective (emotional) consciousness is marked by an advanced capacity for operant learning about rewards and punishments. Our second assumption is that image-based conscious experience is marked by demonstrably mapped representations of the external environment within the body. Certain animals fit both of these criteria, but plants fit neither. We conclude that claims for plant consciousness are highly speculative and lack sound scientific support.
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Affiliation(s)
- Jon Mallatt
- The University of Washington WWAMI Medical Education Program at The University of Idaho, Moscow, ID, 83844, USA.
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Andreas Draguhn
- Institute for Physiology and Pathophysiology, Medical Faculty, University of Heidelberg, 69120, Heidelberg, Germany
| | - David G Robinson
- Centre for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany
| | - Lincoln Taiz
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
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27
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Mutuku JM, Cui S, Yoshida S, Shirasu K. Orobanchaceae parasite-host interactions. THE NEW PHYTOLOGIST 2021; 230:46-59. [PMID: 33202061 DOI: 10.1111/nph.17083] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Parasitic plants in the family Orobanchaceae, such as Striga, Orobanche and Phelipanche, often cause significant damage to agricultural crops. The Orobanchaceae family comprises more than 2000 species in about 100 genera, providing an excellent system for studying the molecular basis of parasitism and its evolution. Notably, the establishment of model Orobanchaceae parasites, such as Triphysaria versicolor and Phtheirospermum japonicum, that can infect the model host Arabidopsis, has greatly facilitated transgenic analyses of genes important for parasitism. In addition, recent genomic and transcriptomic analyses of several Orobanchaceae parasites have revealed fascinating molecular insights into the evolution of parasitism and strategies for adaptation in this family. This review highlights recent progress in understanding how Orobanchaceae parasites attack their hosts and how the hosts mount a defense against the threats.
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Affiliation(s)
- J Musembi Mutuku
- The Central and West African Virus Epidemiology (WAVE). Pôle Scientifique et d'Innovation de Bingerville, Université Félix Houphouët-Boigny, BP V34, Abidjan, 01, Côte d'Ivoire
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Songkui Cui
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoko Yoshida
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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28
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Root stem cells: how to establish and maintain the eternal youth. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2020. [DOI: 10.1007/s12210-020-00893-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Vissenberg K, Gonzalez N. Plant organ and tip growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2363-2364. [PMID: 32324242 PMCID: PMC7178413 DOI: 10.1093/jxb/eraa163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Kris Vissenberg
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
- Plant Biochemistry and Biotechnology Lab, Department of Agriculture, Hellenic Mediterranean University, Heraklion, Crete, Greece
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