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Han E, Geng Z, Qin Y, Wang Y, Ma S. Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism. PLANT COMMUNICATIONS 2024; 5:100978. [PMID: 38783601 PMCID: PMC11369779 DOI: 10.1016/j.xplc.2024.100978] [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: 01/03/2024] [Revised: 03/24/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
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Affiliation(s)
- Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yue Qin
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yuewei Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Shisong Ma
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230027, China.
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2
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Upadhyay-Tiwari N, Huang XJ, Lee YC, Singh SK, Hsu CC, Huang SS, Verslues PE. The nonphototrophic hypocotyl 3 (NPH3) domain protein NRL5 is a trafficking-associated GTPase essential for drought resistance. SCIENCE ADVANCES 2024; 10:eado5429. [PMID: 39121213 PMCID: PMC11313873 DOI: 10.1126/sciadv.ado5429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/02/2024] [Indexed: 08/11/2024]
Abstract
The mechanisms of plant drought resistance are unclear but may involve membrane trafficking and metabolic reprogramming, including proline accumulation. Forward genetic screening using a proline dehydrogenase 1 (ProDH1) promoter:reporter identified a drought hypersensitive mutant with a single-amino acid substitution (P335L) in the nonphototrophic hypocotyl 3 (NPH3) domain of NPH3/root phototropism 2-like 5 (NRL5)/naked pins in Yucca 8 (NPY8). Further experiments found that NRL5 and other NPH3 domain proteins are guanosine triphosphatases (GTPases). NRL5, but not NRL5P335L, interacted with the RABE1c and RABH1b GTPases and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) Vesicle-Associated Membrane Protein (VAMP)721/722. These proteins controlled NRL5 localization and connection to trafficking while also being genetically downstream of, and potentially regulated by, NRL5. These data demonstrate that NRL5-mediated restraint of proline catabolism is required for drought resistance and also reveal unexpected functions of the NPH3 domain such that the role of NPH3 domain proteins in signaling, trafficking, and cellular polarity can be critically reevaluated.
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Affiliation(s)
| | - Xin-Jie Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | | | | | - Shih-Shan Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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3
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Montes C, Zhang J, Nolan TM, Walley JW. Single-cell proteomics differentiates Arabidopsis root cell types. THE NEW PHYTOLOGIST 2024. [PMID: 38923440 DOI: 10.1111/nph.19923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
Single-cell proteomics (SCP) is an emerging approach to resolve cellular heterogeneity within complex tissues of multi-cellular organisms. Here, we demonstrate the feasibility of SCP on plant samples using the model plant Arabidopsis thaliana. Specifically, we focused on examining isolated single cells from the cortex and endodermis, which are two adjacent root cell types derived from a common stem cell lineage. From 756 root cells, we identified 3763 proteins and 1118 proteins/cell. Ultimately, we focus on 3217 proteins quantified following stringent filtering. Of these, we identified 596 proteins whose expression is enriched in either the cortex or endodermis and are able to differentiate these closely related plant cell types. Collectivity, this study demonstrates that SCP can resolve neighboring cell types with distinct functions, thereby facilitating the identification of biomarkers and candidate proteins to enable functional genomics.
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Affiliation(s)
- Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Jingyuan Zhang
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011, USA
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4
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Zeng W, Wang X, Li M. PINOID-centered genetic interactions mediate auxin action in cotyledon formation. PLANT DIRECT 2024; 8:e587. [PMID: 38766507 PMCID: PMC11099747 DOI: 10.1002/pld3.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
Auxin plays a key role in plant growth and development through auxin local synthesis, polar transport, and auxin signaling. Many previous reports on Arabidopsis have found that various types of auxin-related genes are involved in the development of the cotyledon, including the number, symmetry, and morphology of the cotyledon. However, the molecular mechanism by which auxin is involved in cotyledon formation remains to be elucidated. PID, which encodes a serine/threonine kinase localized to the plasma membrane, has been found to phosphorylate the PIN1 protein and regulate its polar distribution in the cell. The loss of function of pid resulted in an abnormal number of cotyledons and defects in inflorescence. It was interesting that the pid mutant interacted synergistically with various types of mutant to generate the severe developmental defect without cotyledon. PID and these genes were indicated to be strongly correlated with cotyledon formation. In this review, PID-centered genetic interactions, related gene functions, and corresponding possible pathways are discussed, providing a perspective that PID and its co-regulators control cotyledon formation through multiple pathways.
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Affiliation(s)
- Wei Zeng
- College of Life ScienceXinyang Normal UniversityXinyangChina
| | - Xiutao Wang
- College of Life ScienceXinyang Normal UniversityXinyangChina
| | - Mengyuan Li
- College of Life ScienceXinyang Normal UniversityXinyangChina
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5
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Liang Z, Xi N, Liu T, Li M, Sang M, Zou C, Chen Z, Yuan G, Pan G, Ma L, Shen Y. A combination of QTL mapping and genome-wide association study revealed the key gene for husk number in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:112. [PMID: 38662228 DOI: 10.1007/s00122-024-04617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/07/2024] [Indexed: 04/26/2024]
Abstract
KEY MESSAGE Two key genes Zm00001d021232 and Zm00001d048138 were identified by QTL mapping and GWAS. Additionally, they were verified to be significantly associated with maize husk number (HN) using gene-based association study. As a by-product of maize production, maize husk is an important industrial raw material. Husk layer number (HN) is an important trait that affects the yield of maize husk. However, the genetic mechanism underlying HN remains unclear. Herein, a total of 13 quantitative trait loci (QTL) controlling HN were identified in an IBM Syn 10 DH population across different locations. Among these, three QTL were individually repeatedly detected in at least two environments. Meanwhile, 26 unique single nucleotide polymorphisms (SNPs) were detected to be significantly (p < 2.15 × 10-6) associated with HN in an association pool. Of these SNPs, three were simultaneously detected across multiple environments or environments and best linear unbiased prediction (BLUP). We focused on these environment-stable and population-common genetic loci for excavating the candidate genes responsible for maize HN. Finally, 173 initial candidate genes were identified, of which 22 were involved in both multicellular organism development and single-multicellular organism process and thus confirmed as the candidate genes for HN. Gene-based association analyses revealed that the variants in four genes were significantly (p < 0.01/N) correlated with HN, of which Zm00001d021232 and Zm00001d048138 were highly expressed in husks and early developing ears among different maize tissues. Our study contributes to the understanding of genetic and molecular mechanisms of maize husk yield and industrial development in the future.
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Affiliation(s)
- Zhenjuan Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Na Xi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minglin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengxiang Sang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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6
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Lanassa Bassukas AE, Xiao Y, Schwechheimer C. Phosphorylation control of PIN auxin transporters. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102146. [PMID: 34974229 DOI: 10.1016/j.pbi.2021.102146] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 06/14/2023]
Abstract
The directional transport of the phytohormone auxin is required for proper plant development and tropic growth. Auxin cell-to-cell transport gains directionality through the polar distribution of 'canonical' long PIN-FORMED (PIN) auxin efflux carriers. In recent years, AGC kinases, MAP kinases, Ca2+/CALMODULIN-DEPENDENT PROTEIN KINASE-RELATED KINASEs and receptor kinases have been implicated in the control of PIN activity, polarity and trafficking. In this review, we summarize the current knowledge in understanding the posttranslational regulation of PINs by these different protein kinase families. The proposed regulation of PINs by AGC kinases after salt stress and by the stress-activated MAP kinases suggest that abiotic and biotic stress factors may modulate auxin transport and thereby plant growth.
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Affiliation(s)
- Alkistis E Lanassa Bassukas
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 8, 85354, Freising, Germany
| | - Yao Xiao
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 8, 85354, Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 8, 85354, Freising, Germany.
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7
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Ramalho JJ, Jones VAS, Mutte S, Weijers D. Pole position: How plant cells polarize along the axes. THE PLANT CELL 2022; 34:174-192. [PMID: 34338785 PMCID: PMC8774072 DOI: 10.1093/plcell/koab203] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/30/2021] [Indexed: 05/10/2023]
Abstract
Having a sense of direction is a fundamental cellular trait that can determine cell shape, division orientation, or function, and ultimately the formation of a functional, multicellular body. Cells acquire and integrate directional information by establishing discrete subcellular domains along an axis with distinct molecular profiles, a process known as cell polarization. Insight into the principles and mechanisms underlying cell polarity has been propelled by decades of extensive research mostly in yeast and animal models. Our understanding of cell polarity establishment in plants, which lack most of the regulatory molecules identified in other eukaryotes, is more limited, but significant progress has been made in recent years. In this review, we explore how plant cells coordinately establish stable polarity axes aligned with the organ axes, highlighting similarities in the molecular logic used to polarize both plant and animal cells. We propose a classification system for plant cell polarity events and nomenclature guidelines. Finally, we provide a deep phylogenetic analysis of polar proteins and discuss the evolution of polarity machineries in plants.
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Affiliation(s)
| | | | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6703WE Wageningen, The Netherlands
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8
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Marhava P. Recent developments in the understanding of PIN polarity. THE NEW PHYTOLOGIST 2022; 233:624-630. [PMID: 34882802 DOI: 10.1111/nph.17867] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/05/2021] [Indexed: 05/20/2023]
Abstract
Polar localization of PIN-FORMED proteins (PINs) at the plasma membrane is essential for plant development as they direct the transport of phytohormone auxin between cells. PIN polar localization to certain sides of a given cell is dynamic, strictly regulated and provides directionality to auxin flow. Signals that act upstream to control subcellular PIN localization modulate auxin distribution, thereby regulating diverse aspects of plant development. Here I summarize the current understanding of mechanisms by which PIN polarity is established, maintained and rearranged to provide a glimpse into the complexity of PIN polarity.
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Affiliation(s)
- Petra Marhava
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
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9
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Verslues PE, Longkumer T. Size and activity of the root meristem: A key for drought resistance and a key model of drought-related signaling. PHYSIOLOGIA PLANTARUM 2022; 174:e13622. [PMID: 34988997 DOI: 10.1111/ppl.13622] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Plants make many adjustments to their growth and development in response to even small changes in water availability. Under such conditions, root elongation can be actively restricted by stress-related signaling mechanisms. Here we look at how the Arabidopsis thaliana root meristem can be affected by moderate water limitation (low water potential, ψw ). Recent characterization of the clade E Growth-Regulating (EGR) protein phosphatases and Microtubule Associated Stress Protein 1 (MASP1) provides an example of how active restriction of root meristem size allows the plant to downregulate root elongation during low ψw stress. EGR2 protein accumulation in cortex cells of the transition zone at the distal end of the root meristem illustrates how the balance of cell division versus cell expansion signals at this critical location can determine meristem size and root elongation during low ψw . These characteristics of EGRs also raise the question of whether they may also be involved in hydrotropism, and, more broadly, whether hydrotropism is a distinct response or a specific manifestation of more general mechanisms used to adjust root growth under moderate severity low ψw whether or not a gradient of water availability is present. These questions, as well as a better understanding of how specific cell layers (cortex and endodermis) seem to have an outsized role in growth regulation and better understanding the roles of plasma membrane-based signaling and polar-localized proteins in the regulation of root meristem size and cell division activity are key to elucidating the cellular mechanisms that determine root growth behavior during soil drying.
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Affiliation(s)
- Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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10
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Light-triggered and phosphorylation-dependent 14-3-3 association with NON-PHOTOTROPIC HYPOCOTYL 3 is required for hypocotyl phototropism. Nat Commun 2021; 12:6128. [PMID: 34675219 PMCID: PMC8531446 DOI: 10.1038/s41467-021-26332-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022] Open
Abstract
NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) is a key component of the auxin-dependent plant phototropic growth response. We report that NPH3 directly binds polyacidic phospholipids, required for plasma membrane association in darkness. We further demonstrate that blue light induces an immediate phosphorylation of a C-terminal 14-3-3 binding motif in NPH3. Subsequent association of 14-3-3 proteins is causal for the light-induced release of NPH3 from the membrane and accompanied by NPH3 dephosphorylation. In the cytosol, NPH3 dynamically transitions into membraneless condensate-like structures. The dephosphorylated state of the 14-3-3 binding site and NPH3 membrane recruitment are recoverable in darkness. NPH3 variants that constitutively localize either to the membrane or to condensates are non-functional, revealing a fundamental role of the 14-3-3 mediated dynamic change in NPH3 localization for auxin-dependent phototropism. This regulatory mechanism might be of general nature, given that several members of the NPH3-like family interact with 14-3-3 via a C-terminal motif. NPH3 is required for auxin-dependent plant phototropism. Here Reuter et al. show that NPH3 is a plasma membrane-bound phospholipid-binding protein and that in response to blue light, NPH3 is phosphorylated and associates with 14-3-3 proteins which leads to dissociation from the plasma membrane.
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11
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Sullivan S, Waksman T, Paliogianni D, Henderson L, Lütkemeyer M, Suetsugu N, Christie JM. Regulation of plant phototropic growth by NPH3/RPT2-like substrate phosphorylation and 14-3-3 binding. Nat Commun 2021; 12:6129. [PMID: 34675214 PMCID: PMC8531357 DOI: 10.1038/s41467-021-26333-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022] Open
Abstract
Polarity underlies all directional growth responses in plants including growth towards the light (phototropism). The plasma-membrane associated protein, NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) is a key determinant of phototropic growth which is regulated by phototropin (phot) AGC kinases. Here we demonstrate that NPH3 is directly phosphorylated by phot1 within a conserved C-terminal consensus sequence (RxS) that is necessary to promote phototropism and petiole positioning in Arabidopsis. RxS phosphorylation also triggers 14-3-3 binding combined with changes in NPH3 phosphorylation and localisation status. Mutants of NPH3 that are unable to bind or constitutively bind 14-3-3 s show compromised functionality consistent with a model where phototropic curvature is established by signalling outputs arising from a gradient of NPH3 RxS phosphorylation across the stem. Our findings therefore establish that NPH3/RPT2-Like (NRL) proteins are phosphorylation targets for plant AGC kinases. Moreover, RxS phosphorylation is conserved in other members of the NRL family, suggesting a common mechanism of regulating plant growth to the prevailing light environment.
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Affiliation(s)
- Stuart Sullivan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Thomas Waksman
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Dimitra Paliogianni
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Louise Henderson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Melanie Lütkemeyer
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK.,RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Noriyuki Suetsugu
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK.,Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - John M Christie
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK.
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12
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Deslauriers SD. High-resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis in Arabidopsis thaliana. AOB PLANTS 2021; 13:plab063. [PMID: 34729159 PMCID: PMC8557632 DOI: 10.1093/aobpla/plab063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
A primary component of seedling establishment is the photomorphogenic response as seedlings emerge from the soil. This process is characterized by a reduced growth rate in the hypocotyl, increased root growth, opening of the apical hook and expansion of the cotyledons as photosynthetic organs. While fundamental to plant success, the photomorphogenic response can be highly variable. Additionally, studies of Arabidopsis thaliana are made difficult by subtle differences in growth rate between individuals. High-resolution imaging and computational processing have emerged as useful tools for quantification of such phenotypes. This study sought to: (i) develop an imaging methodology which could capture changes in growth rate as seedlings transition from darkness to blue light in real time, and (ii) apply this methodology to single-quantitative trait locus (QTL) analysis using the Cvi × Ler recombinant inbred line (RIL) mapping population. Significant differences in the photomorphogenic response were observed between the parent lines and analysis of 158 RILs revealed a wide range of growth rate phenotypes. Quantitative trait locus analysis detected significant loci associated with dark growth rate on chromosome 5 and significant loci associated with light growth rate on chromosome 2. Candidate genes associated with these loci, such as the previously characterized ER locus, highlight the application of this approach for QTL analysis. Genetic analysis of Landsberg lines without the erecta mutation also supports a role for ER in modulating the photomorphogenic response, consistent with previous QTL analyses of this population. Strengths and limitations of this methodology are presented, as well as means of improvement.
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Affiliation(s)
- Stephen D Deslauriers
- Division of Science and Math, University of Minnesota, Morris, Morris, MN 56267, USA
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13
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Integrating the Roles for Cytokinin and Auxin in De Novo Shoot Organogenesis: From Hormone Uptake to Signaling Outputs. Int J Mol Sci 2021; 22:ijms22168554. [PMID: 34445260 PMCID: PMC8395325 DOI: 10.3390/ijms22168554] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/01/2022] Open
Abstract
De novo shoot organogenesis (DNSO) is a procedure commonly used for the in vitro regeneration of shoots from a variety of plant tissues. Shoot regeneration occurs on nutrient media supplemented with the plant hormones cytokinin (CK) and auxin, which play essential roles in this process, and genes involved in their signaling cascades act as master regulators of the different phases of shoot regeneration. In the last 20 years, the genetic regulation of DNSO has been characterized in detail. However, as of today, the CK and auxin signaling events associated with shoot regeneration are often interpreted as a consequence of these hormones simply being present in the regeneration media, whereas the roles for their prior uptake and transport into the cultivated plant tissues are generally overlooked. Additionally, sucrose, commonly added to the regeneration media as a carbon source, plays a signaling role and has been recently shown to interact with CK and auxin and to affect the efficiency of shoot regeneration. In this review, we provide an integrative interpretation of the roles for CK and auxin in the process of DNSO, adding emphasis on their uptake from the regeneration media and their interaction with sucrose present in the media to their complex signaling outputs that mediate shoot regeneration.
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Dümmer M, Spasić SZ, Feil M, Michalski C, Forreiter C, Galland P. Tangent algorithm for photogravitropic balance in plants and Phycomyces blakesleeanus: Roles for EHB1 and NPH3 of Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2021; 260:153396. [PMID: 33713940 DOI: 10.1016/j.jplph.2021.153396] [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: 08/28/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Plant organs that are exposed to continuous unilateral light reach in the steady-state a photogravitropic bending angle that results from the mutual antagonism between the photo- and gravitropic responses. To characterize the interaction between the two tropisms and their quantitative relationship we irradiated seedlings of Arabidopsis thaliana that were inclined at various angles and determined the fluence rates of unilateral blue light required to compensate the gravitropism of the inclined hypocotyls. We found the compensating fluence rates to increase with the tangent of the inclination angles (0° < γ < 90° or max. 120°) and decrease with the cotangent (90°< γ < 180° or max. 120°of the inclination angles. The tangent dependence became also evident from analysis of previous data obtained with Avena sativa and the phycomycete fungus, Phycomyces blakesleeanus. By using loss-of function mutant lines of Arabidopsis, we identified EHB1 (enhanced bending 1) as an essential element for the generation of the tangent and cotangent relationships. Because EHB1 possesses a C2-domain with two putative calcium binding sites, we propose that the ubiquitous calcium dependence of gravi- and phototropism is in part mediated by Ca2+-bound EHB1. Based on a yeast-two-hybrid analysis we found evidence that EHB1 does physically interact with the ARF-GAP protein AGD12. Both proteins were reported to affect gravi- and phototropism antagonistically. We further showed that only AGD12, but not EHB1, interacts with its corresponding ARF-protein. Evidence is provided that AGD12 is able to form homodimers as well as heterodimers with EHB1. On the basis of these data we present a model for a mechanism of early tropism events, in which Ca2+-activated EHB1 emerges as the central processor-like element that links the gravi- and phototropic transduction chains and that generates in coordination with NPH3 and AGD12 the tangent / cotangent algorithm governing photogravitropic equilibrium.
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Affiliation(s)
- Michaela Dümmer
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032, Marburg, Germany.
| | - Sladjana Z Spasić
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, Belgrade, Serbia; Singidunum University, Danijelova 32, Belgrade, Serbia.
| | - Martin Feil
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032, Marburg, Germany.
| | - Christian Michalski
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032, Marburg, Germany.
| | - Christoph Forreiter
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032, Marburg, Germany; Institut für Biologie, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, Adolf-Reichwein Str. 2, D-57068, Siegen, Germany.
| | - Paul Galland
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032, Marburg, Germany.
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15
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Abstract
PIN-FORMED (PIN) polar protein localization directs transport of the growth and developmental regulator auxin in plants. Once established after cytokinesis, PIN polarity requires maintenance. Now, direct interactions between PIN, MAB4/MEL and PID proteins suggest self-reinforced maintenance of PIN polarity through limiting lateral diffusion.
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Affiliation(s)
- Michael Sauer
- Institute of Biochemistry and Biology, Plant Physiology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, DE-14476 Potsdam-Golm, Germany
| | - Markus Grebe
- Institute of Biochemistry and Biology, Plant Physiology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, DE-14476 Potsdam-Golm, Germany.
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16
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Glanc M, Van Gelderen K, Hoermayer L, Tan S, Naramoto S, Zhang X, Domjan D, Včelařová L, Hauschild R, Johnson A, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnár G, Fendrych M, De Rybel B, Offringa R, Friml J. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Curr Biol 2021; 31:1918-1930.e5. [PMID: 33705718 PMCID: PMC8112251 DOI: 10.1016/j.cub.2021.02.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/22/2021] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development. MAB4/MEL proteins are recruited to the plasma membrane by PINs PINs, MAB4/MELs, and AGC kinases directly interact in a multiprotein complex PIN phosphorylation and MAB4/MEL recruitment form a positive feedback loop MAB4/MELs and AGC kinases maintain PIN polarity by limiting PIN lateral diffusion
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Affiliation(s)
- Matouš Glanc
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria; Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague, Czechia; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Kasper Van Gelderen
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas Hoermayer
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Shutang Tan
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Satoshi Naramoto
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Xixi Zhang
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - David Domjan
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Ludmila Včelařová
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Robert Hauschild
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Alexander Johnson
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Edward de Koning
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands
| | - Maritza van Dop
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands
| | - Eike Rademacher
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands
| | - Stef Janson
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands
| | - Xiaoyu Wei
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands
| | - Gergely Molnár
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, (BOKU), 1190 Vienna, Austria
| | - Matyáš Fendrych
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria; Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague, Czechia
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, the Netherlands.
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria.
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17
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Pérez-Pastrana J, Testillano PS, Barany I, Canto-Flick A, Álvarez-López D, Pijeira-Fernández G, Avilés-Viñas SA, Peña-Yam L, Muñoz-Ramírez L, Nahuat-Dzib S, Islas-Flores I, Santana-Buzzy N. Endogenous auxin accumulation/localization during zygotic and somatic embryogenesis of Capsicum chinense Jacq. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153333. [PMID: 33581559 DOI: 10.1016/j.jplph.2020.153333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Zygotic and somatic embryogenesis in plants is a fascinating event that is finely regulated through the expression of a specific group of genes and dynamic levels of plant hormones whose concerted action determines the fate that specific cells follow towards zygotic or somatic embryo development. This work studied different stages of Capsicum chinense Jacq. zygotic and somatic embryogenesis. HPLC quantification determined that the levels of indole-3-acetic acid (IAA) increase as the zygotic or somatic embryogenesis progresses, being higher at maturity, thus supporting a positive correlation between embryo cell differentiation and IAA increase. A monoclonal anti-IAA-antibody was used to detect IAA levels. Findings revealed a dynamic pattern of auxin distribution along the different embryogenic embryonic stages. In the early stages of zygotic embryos, the IAA gradient was observed in the basal cells of the suspensor and the hypostases, suggesting that they are the initial source of the IAA hormone. As embryogenesis proceeds, the dynamic of the IAA gradient is displaced to the embryo and endosperm cells. In the case of induced somatic embryogenesis, the IAA gradient was detected in the dividing cells of the endodermis, from where pre-embryogenic cells emerge. However, the analysis of somatic embryos revealed that IAA was homogeneously distributed. This study shows evidence supporting a correlation between IAA levels during zygotic or somatic embryogenesis in Capsicum chinense species.
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Affiliation(s)
- Jacobo Pérez-Pastrana
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Pilar S Testillano
- Pollen biotechnology of crop plants group, Centro de Investigaciones Biológicas-CSIC, Ramiro Maeztu 9, 28040, Madrid, Spain
| | - Ivett Barany
- Pollen biotechnology of crop plants group, Centro de Investigaciones Biológicas-CSIC, Ramiro Maeztu 9, 28040, Madrid, Spain
| | - Adriana Canto-Flick
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Dulce Álvarez-López
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130 x 32 y 34, colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Gema Pijeira-Fernández
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Susana A Avilés-Viñas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Laura Peña-Yam
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Liliana Muñoz-Ramírez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Sara Nahuat-Dzib
- Laboratorio de Biotecnología, Departamento Ingeniería Química-Bioquímica, TecNM/ Instituto Tecnológico de Mérida, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico.
| | - Nancy Santana-Buzzy
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico.
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18
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Tan S, Luschnig C, Friml J. Pho-view of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling. MOLECULAR PLANT 2021; 14:151-165. [PMID: 33186755 DOI: 10.1016/j.molp.2020.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/07/2020] [Accepted: 11/07/2020] [Indexed: 05/24/2023]
Abstract
The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.
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Affiliation(s)
- Shutang Tan
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.
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19
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Li H, von Wangenheim D, Zhang X, Tan S, Darwish‐Miranda N, Naramoto S, Wabnik K, De Rycke R, Kaufmann WA, Gütl D, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 229:351-369. [PMID: 32810889 PMCID: PMC7984064 DOI: 10.1111/nph.16887] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/07/2020] [Indexed: 05/12/2023]
Abstract
Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN-FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear. Here, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze-fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains. Pharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell-wall components as well as connections between the cell wall and the plasma membrane. This study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems.
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Affiliation(s)
- Hongjiang Li
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
| | - Daniel von Wangenheim
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
- Centre for Plant Integrative BiologySchool of BiosciencesUniversity of NottinghamLoughboroughLE12 5RDUK
| | - Xixi Zhang
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life Sciences (BOKU)Vienna1190Austria
| | - Shutang Tan
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
| | | | - Satoshi Naramoto
- Graduate School of Life SciencesTohoku UniversitySendai980‐8577Japan
| | - Krzysztof Wabnik
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- VIB Center for Plant Systems BiologyGhent9052Belgium
- Expertise Centre for Transmission Electron Microscopy and VIB BioImaging CoreGhent UniversityGhent9052Belgium
| | - Walter A. Kaufmann
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
| | - Daniel Gütl
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
| | - Ricardo Tejos
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Departamento de BiologíaFacultad de CienciasCentro de Biología Molecular VegetalUniversidad de ChileSantiago7800003Chile
| | - Peter Grones
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
| | - Meiyu Ke
- Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Xu Chen
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Jan Dettmer
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria)Klosterneuburg3400Austria
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20
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Shao YJ, Zhu QY, Yao ZW, Liu JX. Phosphoproteomic Analysis of Thermomorphogenic Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:753148. [PMID: 34603364 PMCID: PMC8481946 DOI: 10.3389/fpls.2021.753148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 05/07/2023]
Abstract
Plants rapidly adapt to elevated ambient temperature by adjusting their growth and developmental programs. To date, a number of experiments have been carried out to understand how plants sense and respond to warm temperatures. However, how warm temperature signals are relayed from thermosensors to transcriptional regulators is largely unknown. To identify new early regulators of plant thermo-responsiveness, we performed phosphoproteomic analysis using TMT (Tandem Mass Tags) labeling and phosphopeptide enrichment with Arabidopsis etiolated seedlings treated with or without 3h of warm temperatures (29°C). In total, we identified 13,160 phosphopeptides in 5,125 proteins with 10,700 quantifiable phosphorylation sites. Among them, 200 sites (180 proteins) were upregulated, while 120 sites (87 proteins) were downregulated by elevated temperature. GO (Gene Ontology) analysis indicated that phosphorelay-related molecular function was enriched among the differentially phosphorylated proteins. We selected ATL6 (ARABIDOPSIS TOXICOS EN LEVADURA 6) from them and expressed its native and phosphorylation-site mutated (S343A S357A) forms in Arabidopsis and found that the mutated form of ATL6 was less stable than that of the native form both in vivo and in cell-free degradation assays. Taken together, our data revealed extensive protein phosphorylation during thermo-responsiveness, providing new candidate proteins/genes for studying plant thermomorphogenesis in the future.
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21
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AT-Hook Transcription Factors Restrict Petiole Growth by Antagonizing PIFs. Curr Biol 2020; 30:1454-1466.e6. [DOI: 10.1016/j.cub.2020.02.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 10/26/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
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22
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Kato M, Tsuge T, Maeshima M, Aoyama T. Arabidopsis PCaP2 modulates the phosphatidylinositol 4,5-bisphosphate signal on the plasma membrane and attenuates root hair elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:610-625. [PMID: 30604455 DOI: 10.1111/tpj.14226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 05/22/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2 ] serves as a subcellular signal on the plasma membrane, mediating various cell-polarized phenomena including polar cell growth. Here, we investigated the involvement of Arabidopsis thaliana PCaP2, a plant-unique plasma membrane protein with phosphoinositide-binding activity, in PtdIns(4,5)P2 signaling for root hair tip growth. The long-root-hair phenotype of the pcap2 knockdown mutant was found to stem from its higher average root hair elongation rate compared with the wild type and to counteract the low average rate caused by a defect in the PtdIns(4,5)P2 -producing enzyme gene PIP5K3. On the plasma membrane of elongating root hairs, the PCaP2 promoter-driven PCaP2-green fluorescent protein (GFP), which complemented the pcap2 mutant phenotype, overlapped with the PtdIns(4,5)P2 marker 2xCHERRY-2xPHPLC in the subapical region, but not at the apex, suggesting that PCaP2 attenuates root hair elongation via PtdIns(4,5)P2 signaling on the subapical plasma membrane. Consistent with this, a GFP fusion with the PCaP2 phosphoinositide-binding domain PCaP2N23 , root hair-specific overexpression of which caused a low average root hair elongation rate, localized more intense to the subapical plasma membrane than to the apical plasma membrane similar to PCaP2-GFP. Inducibly overexpressed PCaP2-GFP, but not its derivative lacking the PCaP2N23 domain, replaced 2xCHERRY-2xPHPLC on the plasma membrane in root meristematic epidermal cells, and suppressed FM4-64 internalization in elongating root hairs. Moreover, inducibly overexpressed PCaP2 arrested an endocytic process of PIN2-GFP recycling. Based on these results, we conclude that PCaP2 functions as a negative modulator of PtdIns(4,5)P2 signaling on the subapical plasma membrane probably through competitive binding to PtdIns(4,5)P2 and attenuates root hair elongation.
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Affiliation(s)
- Mariko Kato
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Masayoshi Maeshima
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, 464-8601, Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
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23
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Glanc M, Fendrych M, Friml J. PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton. Biomolecules 2019; 9:biom9060222. [PMID: 31181636 PMCID: PMC6628292 DOI: 10.3390/biom9060222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022] Open
Abstract
Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.
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Affiliation(s)
- Matouš Glanc
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria.
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague, Czech Republic.
| | - Matyáš Fendrych
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria.
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague, Czech Republic.
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria.
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24
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Sessa G, Carabelli M, Possenti M, Morelli G, Ruberti I. Multiple Links between HD-Zip Proteins and Hormone Networks. Int J Mol Sci 2018; 19:ijms19124047. [PMID: 30558150 PMCID: PMC6320839 DOI: 10.3390/ijms19124047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 01/01/2023] Open
Abstract
HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.
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Affiliation(s)
- Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Monica Carabelli
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
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Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. NATURE PLANTS 2018; 4:1082-1088. [PMID: 30518833 PMCID: PMC6394824 DOI: 10.1038/s41477-018-0318-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/01/2018] [Indexed: 05/19/2023]
Abstract
Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate-a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2-5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.
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Affiliation(s)
- Matouš Glanc
- IST Austria, Klosterneuburg, Austria
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Matyáš Fendrych
- IST Austria, Klosterneuburg, Austria
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
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Barbosa ICR, Hammes UZ, Schwechheimer C. Activation and Polarity Control of PIN-FORMED Auxin Transporters by Phosphorylation. TRENDS IN PLANT SCIENCE 2018; 23:523-538. [PMID: 29678589 DOI: 10.1016/j.tplants.2018.03.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/11/2018] [Accepted: 03/14/2018] [Indexed: 05/09/2023]
Abstract
Auxin controls almost every aspect of plant development. Auxin is distributed within the plant by passive diffusion and active cell-to-cell transport. PIN-FORMED (PIN) auxin efflux transporters are polarly distributed in the plasma membranes of many cells, and knowledge about their distribution can predict auxin transport and explain auxin distribution patterns, even in complex tissues. Recent studies have revealed that phosphorylation is essential for PIN activation, suggesting that PIN phosphorylation needs to be taken into account in understanding auxin transport. These findings also ask for a re-examination of previously proposed mechanisms for phosphorylation-dependent PIN polarity control. We provide a comprehensive summary of the current knowledge on PIN regulation by phosphorylation, and discuss possible mechanisms of PIN polarity control in the context of recent findings.
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Affiliation(s)
- Inês C R Barbosa
- Department of Plant Molecular Biology, Biophore Building, Unil-Sorge, Université de Lausanne, 1015 Lausanne, Switzerland; These authors contributed equally to this review article and are listed in alphabetical order
| | - Ulrich Z Hammes
- Plant Systems Biology, Technical University Munich, Emil-Ramann-Strasse 8, 85354 Freising, Germany; These authors contributed equally to this review article and are listed in alphabetical order
| | - Claus Schwechheimer
- Plant Systems Biology, Technical University Munich, Emil-Ramann-Strasse 8, 85354 Freising, Germany; These authors contributed equally to this review article and are listed in alphabetical order.
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Naramoto S. Polar transport in plants mediated by membrane transporters: focus on mechanisms of polar auxin transport. CURRENT OPINION IN PLANT BIOLOGY 2017; 40:8-14. [PMID: 28686910 DOI: 10.1016/j.pbi.2017.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/06/2017] [Accepted: 06/14/2017] [Indexed: 05/08/2023]
Abstract
Directional cell-to-cell transport of functional molecules, called polar transport, enables plants to sense and respond to developmental and environmental signals. Transporters that localize to plasma membranes (PMs) in a polar manner are key components of these systems. PIN-FORMED (PIN) auxin efflux carriers, which are the most studied polar-localized PM proteins, are implicated in the polar transport of auxin that in turn regulates plant development and tropic growth. In this review, the regulatory mechanisms underlying polar localization of PINs, control of auxin efflux activity, and PIN abundance at PMs are considered. Up to date information on polar-localized nutrient transporters that regulate directional nutrient movement from soil into the root vasculature is also discussed.
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Affiliation(s)
- Satoshi Naramoto
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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28
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Du H, Zhu J, Su H, Huang M, Wang H, Ding S, Zhang B, Luo A, Wei S, Tian X, Xu Y. Bulked Segregant RNA-seq Reveals Differential Expression and SNPs of Candidate Genes Associated with Waterlogging Tolerance in Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:1022. [PMID: 28659961 PMCID: PMC5470080 DOI: 10.3389/fpls.2017.01022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/29/2017] [Indexed: 05/24/2023]
Abstract
Waterlogging has increasingly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 waterlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines. BSR-seq was performed to identify differentially expressed genes and SNPs associated with waterlogging tolerance. Upon waterlogging stress, 354 and 1094 genes were differentially expressed in the tolerant and sensitive pools, respectively, compared to untreated controls. When tolerant and sensitive pools were compared, 593 genes were differentially expressed under untreated and 431 genes under waterlogged conditions, of which 122 genes overlapped. To validate the BSR-seq results, the expression levels of six genes were determined by qRT-PCR. The qRT-PCR results were consistent with BSR-seq results. Comparison of allelic polymorphism in mRNA sequences between tolerant and sensitive pools revealed 165 (normal condition) and 128 (waterlogged condition) high-probability SNPs. We found 18 overlapping SNPs with genomic positions mapped. Eighteen SNPs were contained in 18 genes, and eight and nine of 18 genes were responsive to waterlogging stress in tolerant and sensitive lines, respectively. Six alleles of the 18 originated from tolerant pool were significantly up-regulated under waterlogging, but not those from sensitive pool. Importantly, one allele (GRMZM2G055704) of the six genes was mapped between umc1619 and umc1948 on chromosome 1 where a QTL associated with waterlogging tolerance was identified in a previous research, strongly indicating that GRMZM2G055704 is a candidate gene responsive to waterlogging. Our research contributes to the knowledge of the molecular mechanism for waterlogging tolerance in maize.
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Affiliation(s)
- Hewei Du
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
- College of Life Science, Yangtze UniversityJingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze UniversityJingzhou, China
| | - Jianxiong Zhu
- College of Life Science, Yangtze UniversityJingzhou, China
| | - Hang Su
- College of Life Science, Yangtze UniversityJingzhou, China
| | - Ming Huang
- College of Life Science, Yangtze UniversityJingzhou, China
| | - Hongwei Wang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
| | - Shuangcheng Ding
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
| | - Binglin Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
| | - An Luo
- College of Life Science, Yangtze UniversityJingzhou, China
| | - Shudong Wei
- College of Life Science, Yangtze UniversityJingzhou, China
| | - Xiaohai Tian
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
| | - Yunbi Xu
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
- International Maize and Wheat Improvement Center (CIMMYT)Texcoco, Mexico
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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29
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Ghan R, Petereit J, Tillett RL, Schlauch KA, Toubiana D, Fait A, Cramer GR. The common transcriptional subnetworks of the grape berry skin in the late stages of ripening. BMC PLANT BIOLOGY 2017; 17:94. [PMID: 28558655 PMCID: PMC5450095 DOI: 10.1186/s12870-017-1043-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/22/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. CONCLUSIONS A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
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Affiliation(s)
- Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Juli Petereit
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Richard L. Tillett
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Karen A. Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - David Toubiana
- Telekom Innovation, Laboratories and Cyber Security Research Center, Department of Information, Systems Engineering, Ben Gurion University, Beer Sheva, Israel
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, 84990 Midreshet Ben-Gurion, Israel
| | - Grant R. Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
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30
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Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discov 2016; 2:16018. [PMID: 27462465 PMCID: PMC4950145 DOI: 10.1038/celldisc.2016.18] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/11/2016] [Indexed: 01/24/2023] Open
Abstract
The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.
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31
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Armengot L, Marquès-Bueno MM, Jaillais Y. Regulation of polar auxin transport by protein and lipid kinases. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4015-4037. [PMID: 27242371 PMCID: PMC4968656 DOI: 10.1093/jxb/erw216] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The directional transport of auxin, known as polar auxin transport (PAT), allows asymmetric distribution of this hormone in different cells and tissues. This system creates local auxin maxima, minima, and gradients that are instrumental in both organ initiation and shape determination. As such, PAT is crucial for all aspects of plant development but also for environmental interaction, notably in shaping plant architecture to its environment. Cell to cell auxin transport is mediated by a network of auxin carriers that are regulated at the transcriptional and post-translational levels. Here we review our current knowledge on some aspects of the 'non-genomic' regulation of auxin transport, placing an emphasis on how phosphorylation by protein and lipid kinases controls the polarity, intracellular trafficking, stability, and activity of auxin carriers. We describe the role of several AGC kinases, including PINOID, D6PK, and the blue light photoreceptor phot1, in phosphorylating auxin carriers from the PIN and ABCB families. We also highlight the function of some receptor-like kinases (RLKs) and two-component histidine kinase receptors in PAT, noting that there are probably RLKs involved in co-ordinating auxin distribution yet to be discovered. In addition, we describe the emerging role of phospholipid phosphorylation in polarity establishment and intracellular trafficking of PIN proteins. We outline these various phosphorylation mechanisms in the context of primary and lateral root development, leaf cell shape acquisition, as well as root gravitropism and shoot phototropism.
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Affiliation(s)
- Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Maria Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
- Correspondence to:
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32
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Zhang Y, Dong J. Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System. J Vis Exp 2016:53790. [PMID: 27022690 PMCID: PMC4829033 DOI: 10.3791/53790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Visualization of dynamic signaling events in live cells has been a challenge. We expanded an established transient expression system, the biomolecular fluorescent complementation (BiFC) assay in tobacco epidermal cells, from testing protein-protein interaction to monitoring spatial distribution of signal transduction in plant cells. In this protocol, we used the BiFC assay to show that the interaction and the signaling between the Arabidopsis MAPKKK YODA and MAPK6 occur at the plasma membrane. When the scaffold protein BASL was co-expressed, the YODA-MAPK interaction redistributed and spatially co-polarized with CFP-BASL. This modified tobacco expression system allows for quick examination of signaling localization and dynamic changes (less than 4 days) and can accommodate multiple of fluorescent protein colors (at least three). We also presented detailed methods to quantify protein distribution (asymmetric spatial localization, or "polarization") in tobacco cells. This advanced tobacco expression system has a potential to be used widely for quick testing of dynamic signaling events in live plant cells.
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Affiliation(s)
- Ying Zhang
- The Waksman Institute of Microbiology, Rutgers, The State University of New Jersey
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, The State University of New Jersey; The Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey;
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33
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Sluis A, Hake S. Organogenesis in plants: initiation and elaboration of leaves. Trends Genet 2015; 31:300-6. [PMID: 26003219 DOI: 10.1016/j.tig.2015.04.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/24/2022]
Abstract
Plant organs initiate from meristems and grow into diverse forms. After initiation, organs enter a morphological phase where they develop their shape, followed by differentiation into mature tissue. Investigations into these processes have revealed numerous factors necessary for proper development, including transcription factors such as the KNOTTED-LIKE HOMEOBOX (KNOX) genes, the hormone auxin, and miRNAs. Importantly, these factors have been shown to play a role in organogenesis in various diverse model species, revealing both deep conservation of regulatory strategies and evolutionary novelties that led to new plant forms. We review here recent work in understanding the regulation of organogenesis and in particular leaf formation, highlighting how regulatory modules are often redeployed in different organ types and stages of development to achieve diverse forms through the balance of growth and differentiation.
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Affiliation(s)
- Aaron Sluis
- Plant Gene Expression Center, UC Berkeley and USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
| | - Sarah Hake
- Plant Gene Expression Center, UC Berkeley and USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
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34
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Lyons R, Stiller J, Powell J, Rusu A, Manners JM, Kazan K. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana. PLoS One 2015; 10:e0121902. [PMID: 25849296 PMCID: PMC4388846 DOI: 10.1371/journal.pone.0121902] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/05/2015] [Indexed: 11/19/2022] Open
Abstract
Some of the most devastating agricultural diseases are caused by root-infecting pathogens, yet the majority of studies on these interactions to date have focused on the host responses of aerial tissues rather than those belowground. Fusarium oxysporum is a root-infecting pathogen that causes wilt disease on several plant species including Arabidopsis thaliana. To investigate and compare transcriptional changes triggered by F. oxysporum in different Arabidopsis tissues, we infected soil-grown plants with F. oxysporum and subjected root and leaf tissue harvested at early and late timepoints to RNA-seq analyses. At least half of the genes induced or repressed by F. oxysporum showed tissue-specific regulation. Regulators of auxin and ABA signalling, mannose binding lectins and peroxidases showed strong differential expression in root tissue. We demonstrate that ARF2 and PRX33, two genes regulated in the roots, promote susceptibility to F. oxysporum. In the leaves, defensins and genes associated with the response to auxin, cold and senescence were strongly regulated while jasmonate biosynthesis and signalling genes were induced throughout the plant.
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Affiliation(s)
- Rebecca Lyons
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
- * E-mail:
| | - Jiri Stiller
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - Jonathan Powell
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - Anca Rusu
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - John M. Manners
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT, Australia
| | - Kemal Kazan
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture & Food Innovation (QAAFI), The University of Queensland, St Lucia, Brisbane, Queensland, 4067, Australia
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35
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DePaoli HC, Dornelas MC, Goldman MHS. SCI1 is a component of the auxin-dependent control of cell proliferation in Arabidopsis upper pistil. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:122-130. [PMID: 25443839 DOI: 10.1016/j.plantsci.2014.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/04/2014] [Accepted: 09/08/2014] [Indexed: 06/04/2023]
Abstract
To characterize the recently described SCI1 (stigma/style cell cycle inhibitor 1) gene relationship with the auxin pathway, we have taken the advantage of the Arabidopsis model system and its available tools. At first, we have analyzed the At1g79200 T-DNA insertion mutants and constructed various transgenic plants. The loss- and gain-of-function plants displayed cell number alterations in upper pistils that were controlled by the amino-terminal domain of the protein. These data also confirmed that this locus holds the functional homolog (AtSCI1) of the Nicotiana tabacum SCI1 gene. Then, we have provided some evidences the auxin synthesis/signaling pathways are required for downstream proper AtSCI1 control of cell number: (a) its expression is downregulated in yuc2yuc6 and npy1 auxin-deficient mutants, (b) triple (yuc2yuc6sci1) and double (npy1sci1) mutants mimicked the auxin-deficient phenotypes, with no synergistic interactions, and (c) the increased upper pistil phenotype in these last mutants, which is a consequence of an increased cell number, was able to be complemented by AtSCI1 overexpression. Taken together, our data strongly suggests SCI1 as a component of the auxin signaling transduction pathway to control cell proliferation/differentiation in stigma/style, representing a molecular effector of this hormone on pistil development.
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Affiliation(s)
- Henrique Cestari DePaoli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto 14040-901, Brazil; Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA; PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto 14049-900, Brazil
| | - Marcelo Carnier Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
| | - Maria Helena S Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto 14040-901, Brazil.
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Shalom L, Samuels S, Zur N, Shlizerman L, Doron-Faigenboim A, Blumwald E, Sadka A. Fruit load induces changes in global gene expression and in abscisic acid (ABA) and indole acetic acid (IAA) homeostasis in citrus buds. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3029-44. [PMID: 24706719 PMCID: PMC4071824 DOI: 10.1093/jxb/eru148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Many fruit trees undergo cycles of heavy fruit load (ON-Crop) in one year, followed by low fruit load (OFF-Crop) the following year, a phenomenon known as alternate bearing (AB). The mechanism by which fruit load affects flowering induction during the following year (return bloom) is still unclear. Although not proven, it is commonly accepted that the fruit or an organ which senses fruit presence generates an inhibitory signal that moves into the bud and inhibits apical meristem transition. Indeed, fruit removal from ON-Crop trees (de-fruiting) induces return bloom. Identification of regulatory or metabolic processes modified in the bud in association with altered fruit load might shed light on the nature of the AB signalling process. The bud transcriptome of de-fruited citrus trees was compared with those of ON- and OFF-Crop trees. Fruit removal resulted in relatively rapid changes in global gene expression, including induction of photosynthetic genes and proteins. Altered regulatory mechanisms included abscisic acid (ABA) metabolism and auxin polar transport. Genes of ABA biosynthesis were induced; however, hormone analyses showed that the ABA level was reduced in OFF-Crop buds and in buds shortly following fruit removal. Additionally, genes associated with Ca(2+)-dependent auxin polar transport were remarkably induced in buds of OFF-Crop and de-fruited trees. Hormone analyses showed that auxin levels were reduced in these buds as compared with ON-Crop buds. In view of the auxin transport autoinhibition theory, the possibility that auxin distribution plays a role in determining bud fate is discussed.
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Affiliation(s)
- Liron Shalom
- Department of Fruit Trees Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sivan Samuels
- Department of Fruit Trees Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naftali Zur
- Department of Fruit Trees Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Lyudmila Shlizerman
- Department of Fruit Trees Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Adi Doron-Faigenboim
- Department of Fruit Trees Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Avi Sadka
- Department of Fruit Trees Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
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37
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Habets MEJ, Offringa R. PIN-driven polar auxin transport in plant developmental plasticity: a key target for environmental and endogenous signals. THE NEW PHYTOLOGIST 2014; 203:362-377. [PMID: 24863651 DOI: 10.1111/nph.12831] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/01/2014] [Indexed: 05/21/2023]
Abstract
Plants master the art of coping with environmental challenges in two ways: on the one hand, through their extensive defense systems, and on the other, by their developmental plasticity. The plant hormone auxin plays an important role in a plant's adaptations to its surroundings, as it specifies organ orientation and positioning by regulating cell growth and division in response to internal and external signals. Important in auxin action is the family of PIN-FORMED (PIN) auxin transport proteins that generate auxin maxima and minima by driving polar cell-to-cell transport of auxin through their asymmetric subcellular distribution. Here, we review how regulatory proteins, the cytoskeleton, and membrane trafficking affect PIN expression and localization. Transcriptional regulation of PIN genes alters protein abundance, provides tissue-specific expression, and enables feedback based on auxin concentrations and crosstalk with other hormones. Post-transcriptional modification, for example by PIN phosphorylation or ubiquitination, provides regulation through protein trafficking and degradation, changing the direction and quantity of the auxin flow. Several plant hormones affect PIN abundance, resulting in another means of crosstalk between auxin and these hormones. In conclusion, PIN proteins are instrumental in directing plant developmental responses to environmental and endogenous signals.
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Affiliation(s)
- Myckel E J Habets
- Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Remko Offringa
- Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
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38
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Kania U, Fendrych M, Friml J. Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biol 2014; 4:140017. [PMID: 24740985 PMCID: PMC4043115 DOI: 10.1098/rsob.140017] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Although plant and animal cells use a similar core mechanism to deliver proteins
to the plasma membrane, their different lifestyle, body organization and
specific cell structures resulted in the acquisition of regulatory mechanisms
that vary in the two kingdoms. In particular, cell polarity regulators do not
seem to be conserved, because genes encoding key components are absent in plant
genomes. In plants, the broad knowledge on polarity derives from the study of
auxin transporters, the PIN-FORMED proteins, in the model plant
Arabidopsis thaliana. In animals, much information is
provided from the study of polarity in epithelial cells that exhibit basolateral
and luminal apical polarities, separated by tight junctions. In this review, we
summarize the similarities and differences of the polarization mechanisms
between plants and animals and survey the main genetic approaches that have been
used to characterize new genes involved in polarity establishment in plants,
including the frequently used forward and reverse genetics screens as well as a
novel chemical genetics approach that is expected to overcome the limitation of
classical genetics methods.
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Affiliation(s)
- Urszula Kania
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
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39
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MAB4-induced auxin sink generates local auxin gradients in Arabidopsis organ formation. Proc Natl Acad Sci U S A 2014; 111:1198-203. [PMID: 24395791 DOI: 10.1073/pnas.1316109111] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In Arabidopsis, leaves and flowers form cyclically in the shoot meristem periphery and are triggered by local accumulations of the plant hormone auxin. Auxin maxima are established by the auxin efflux carrier PIN-formed1 (PIN1). During organ formation, two distinct types of PIN1 polarization occur. First, convergence of PIN1 polarity in the surface of the meristem creates local auxin peaks. Second, basipetal PIN1 polarization causes auxin to move away from the surface in the middle of an incipient organ primordium, thought to contribute to vascular formation. Several mathematical models have been developed in attempts to explain the PIN1 localization pattern. However, the molecular mechanisms that control these dynamic changes are unknown. Here, we show that loss-of-function in the MACCHI-BOU 4 (MAB4) family genes, which encode nonphototropic hypocotyl 3-like proteins and regulate PIN endocytosis, cause deletion of basipetal PIN1 polarization, resulting in extensive auxin accumulation all over the meristem surface from lack of a sink for auxin. These results indicate that the MAB4 family genes establish inward auxin transport from the L1 surface of incipient organ primordia by basipetal PIN1 polarization, and that this behavior is essential for the progression of organ development. Furthermore, the expression of the MAB4 family genes depends on auxin response. Our results define two distinct molecular mechanisms for PIN1 polarization during organ development and indicate that an auxin response triggers the switching between these two mechanisms.
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40
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Zhang KX, Xu HH, Yuan TT, Zhang L, Lu YT. Blue-light-induced PIN3 polarization for root negative phototropic response in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:308-21. [PMID: 23888933 DOI: 10.1111/tpj.12298] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/04/2013] [Accepted: 07/12/2013] [Indexed: 05/04/2023]
Abstract
Root negative phototropism is an important response in plants. Although blue light is known to mediate this response, the cellular and molecular mechanisms underlying root negative phototropism remain unclear. Here, we report that the auxin efflux carrier PIN-FORMED (PIN) 3 is involved in asymmetric auxin distribution and root negative phototropism. Unilateral blue-light illumination polarized PIN3 to the outer lateral membrane of columella cells at the illuminated root side, and increased auxin activity at the illuminated side of roots, where auxin promotes growth and causes roots bending away from the light source. Furthermore, root negative phototropic response and blue-light-induced PIN3 polarization were modulated by a brefeldin A-sensitive, GNOM-dependent, trafficking pathway and by phot1-regulated PINOID (PID)/PROTEIN PHOSPHATASE 2A (PP2A) activity. Our results indicate that blue-light-induced PIN3 polarization is needed for asymmetric auxin distribution during root negative phototropic response.
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Affiliation(s)
- Kun-Xiao Zhang
- Key Lab of MOE for Plant Development, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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41
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Abstract
E3 ligases comprise a highly diverse and important group of enzymes that act within the 26S ubiquitin proteasome pathway. They facilitate the transfer of ubiquitin moieties to substrate proteins which may be marked for degradation by this step. As such, they serve as central regulators in many cellular and physiological processes in plants. The review provides an update on the multitude of different E3 ligases currently known in plants, and illustrates the central role in plant biology of specific examples.
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Affiliation(s)
- Liyuan Chen
- Plant Stress Physiology, School of Biological Sciences, Abelson 435, PO Box 644236, Washington State University, Pullman, WA 99164-4236, USA
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42
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Offringa R, Huang F. Phosphorylation-dependent trafficking of plasma membrane proteins in animal and plant cells. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:789-808. [PMID: 23945267 DOI: 10.1111/jipb.12096] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/02/2013] [Indexed: 05/27/2023]
Abstract
In both unicellular and multicellular organisms, transmembrane (TM) proteins are sorted to and retained at specific membrane domains by endomembrane trafficking mechanisms that recognize sorting signals in the these proteins. The trafficking and distribution of plasma membrane (PM)-localized TM proteins (PM proteins), especially of those PM proteins that show an asymmetric distribution over the PM, has received much attention, as their proper PM localization is crucial for elementary signaling and transport processes, and defects in their localization often lead to severe disease symptoms or developmental defects. The subcellular localization of PM proteins is dynamically regulated by post-translational modifications, such as phosphorylation and ubiquitination. These modificaitons mostly occur on sorting signals that are located in the larger cytosolic domains of the cargo proteins. Here we review the effects of phosphorylation of PM proteins on their trafficking, and present the key examples from the animal field that have been subject to studies for already several decades, such as that of aquaporin 2 and the epidermal growth factor receptor. Our knowledge on cargo trafficking in plants is largely based on studies of the family of PIN FORMED (PIN) carriers that mediate the efflux of the plant hormone auxin. We will review what is known on the subcellular distribution and trafficking of PIN proteins, with a focus on how this is modulated by phosphorylation, and identify and discuss analogies and differences in trafficking with the well-studied animal examples.
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Affiliation(s)
- Remko Offringa
- Molecular and Developmental Genetics, Institute Biology Leiden, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, Leiden University, The Netherlands
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43
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Genschik P, Sumara I, Lechner E. The emerging family of CULLIN3-RING ubiquitin ligases (CRL3s): cellular functions and disease implications. EMBO J 2013; 32:2307-20. [PMID: 23912815 DOI: 10.1038/emboj.2013.173] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/12/2013] [Indexed: 01/07/2023] Open
Abstract
Protein ubiquitylation is a post-translational modification that controls all aspects of eukaryotic cell functionality, and its defective regulation is manifested in various human diseases. The ubiquitylation process requires a set of enzymes, of which the ubiquitin ligases (E3s) are the substrate recognition components. Modular CULLIN-RING ubiquitin ligases (CRLs) are the most prevalent class of E3s, comprising hundreds of distinct CRL complexes with the potential to recruit as many and even more protein substrates. Best understood at both structural and functional levels are CRL1 or SCF (SKP1/CUL1/F-box protein) complexes, representing the founding member of this class of multimeric E3s. Another CRL subfamily, called CRL3, is composed of the molecular scaffold CULLIN3 and the RING protein RBX1, in combination with one of numerous BTB domain proteins acting as substrate adaptors. Recent work has firmly established CRL3s as major regulators of different cellular and developmental processes as well as stress responses in both metazoans and higher plants. In humans, functional alterations of CRL3s have been associated with various pathologies, including metabolic disorders, muscle, and nerve degeneration, as well as cancer. In this review, we summarize recent discoveries on the function of CRL3s in both metazoans and plants, and discuss their mode of regulation and specificities.
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Affiliation(s)
- Pascal Genschik
- Unité Propre de Recherche 2357, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Conventionné avec l'Université de Strasbourg, Strasbourg, France.
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44
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Goyal A, Szarzynska B, Fankhauser C. Phototropism: at the crossroads of light-signaling pathways. TRENDS IN PLANT SCIENCE 2013; 18:393-401. [PMID: 23562459 DOI: 10.1016/j.tplants.2013.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/28/2013] [Accepted: 03/08/2013] [Indexed: 05/11/2023]
Abstract
Phototropism enables plants to orient growth towards the direction of light and thereby maximizes photosynthesis in low-light environments. In angiosperms, blue-light photoreceptors called phototropins are primarily involved in sensing the direction of light. Phytochromes and cryptochromes (sensing red/far-red and blue light, respectively) also modulate asymmetric hypocotyl growth, leading to phototropism. Interactions between different light-signaling pathways regulating phototropism occur in cryptogams and angiosperms. In this review, we focus on the molecular mechanisms underlying the co-action between photosensory systems in the regulation of hypocotyl phototropism in Arabidopsis thaliana. Recent studies have shown that phytochromes and cryptochromes enhance phototropism by controlling the expression of important regulators of phototropin signaling. In addition, phytochromes may also regulate growth towards light via direct interaction with the phototropins.
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Affiliation(s)
- Anupama Goyal
- Centre for Integrative Genomics, University of Lausanne, Genopode Building, CH 1015 Lausanne, Switzerland
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45
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Gallavotti A. The role of auxin in shaping shoot architecture. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2593-608. [PMID: 23709672 DOI: 10.1093/jxb/ert141] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The variety of plant architectures observed in nature is predominantly determined by vegetative and reproductive branching patterns, the positioning of lateral organs, and differential stem elongation. Branches, lateral organs, and stems are the final products of the activity of meristems, groups of stem cells whose function is genetically determined and environmentally influenced. Several decades of studies in different plant species have shed light on the essential role of the hormone auxin in plant growth and development. Auxin influences stem elongation and regulates the formation, activity, and fate of meristems, and has therefore been recognized as a major hormone shaping plant architecture. Increasing our knowledge of the molecular mechanisms that regulate auxin function is necessary to understand how different plant species integrate a genetically determined developmental programme, the establishment of a body plan, with constant inputs from the surrounding environment. This information will allow us to develop the molecular tools needed to modify plant architecture in several crop species and in rapidly changing environments.
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Affiliation(s)
- Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA.
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46
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Drdová EJ, Synek L, Pečenková T, Hála M, Kulich I, Fowler JE, Murphy AS, Zárský V. The exocyst complex contributes to PIN auxin efflux carrier recycling and polar auxin transport in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:709-19. [PMID: 23163883 DOI: 10.1111/tpj.12074] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 11/07/2012] [Accepted: 11/13/2012] [Indexed: 05/20/2023]
Abstract
In land plants polar auxin transport is one of the substantial processes guiding whole plant polarity and morphogenesis. Directional auxin fluxes are mediated by PIN auxin efflux carriers, polarly localized at the plasma membrane. The polarization of exocytosis in yeast and animals is assisted by the exocyst: an octameric vesicle-tethering complex and an effector of Rab and Rho GTPases. Here we show that rootward polar auxin transport is compromised in roots of Arabidopsis thaliana loss-of-function mutants in the EXO70A1 exocyst subunit. The recycling of PIN1 and PIN2 proteins from brefeldin-A compartments is delayed after the brefeldin-A washout in exo70A1 and sec8 exocyst mutants. Relocalization of PIN1 and PIN2 proteins after prolonged brefeldin-A treatment is largely impaired in these mutants. At the same time, however, plasma membrane localization of GFP:EXO70A1, and the other exocyst subunits studied (GFP:SEC8 and YFP:SEC10), is resistant to brefeldin-A treatment. In root cells of the exo70A1 mutant, a portion of PIN2 is internalized and retained in specific, abnormally enlarged, endomembrane compartments that are distinct from VHA-a1-labelled early endosomes or the trans-Golgi network, but are RAB-A5d positive. We conclude that the exocyst is involved in PIN1 and PIN2 recycling, and thus in polar auxin transport regulation.
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Affiliation(s)
- Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 16502 Prague 6, Czech Republic
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47
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Gupta S, Shi X, Lindquist IE, Devitt N, Mudge J, Rashotte AM. Transcriptome profiling of cytokinin and auxin regulation in tomato root. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:695-704. [PMID: 23307920 PMCID: PMC3542057 DOI: 10.1093/jxb/ers365] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Tomato is a model and economically important crop plant with little information available about gene expression in roots. Currently, there have only been a few studies that examine hormonal responses in tomato roots and none at a genome-wide level. This study examined the transcriptome atlas of tomato root regions (root tip, lateral roots, and whole roots) and the transcriptional regulation of each root region in response to the plant hormones cytokinin and auxin using Illumina RNA sequencing. More than 165 million 1×54 base pair reads were mapped onto the Solanum lycopersicum reference genome and differential expression patterns in each root region in response to each hormone were assessed. Many novel cytokinin- and auxin-induced and -repressed genes were identified as significantly differentially expressed and the expression levels of several were confirmed by qPCR. A number of these regulated genes represent tomato orthologues of cytokinin- or auxin-regulated genes identified in other species, including CKXs, type-A RRs, Aux/IAAs, and ARFs. Additionally, the data confirm some of the hormone regulation studies for recently examined genes in tomato such as SlIAAs and SlGH3s. Moreover, genes expressed abundantly in each root region were identified which provide a spatial distribution of many classes of genes, including plant defence, secondary metabolite production, and general metabolism across the root. Overall this study presents the first global expression patterns of hormone-regulated transcripts in tomato roots, which will be functionally relevant for future studies directed towards tomato root growth and development.
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Affiliation(s)
- Sarika Gupta
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xiuling Shi
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ingrid E. Lindquist
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA
| | - Nicholas Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA
| | - Aaron M. Rashotte
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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48
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Nakamura M, Kiefer CS, Grebe M. Planar polarity, tissue polarity and planar morphogenesis in plants. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:593-600. [PMID: 22906885 DOI: 10.1016/j.pbi.2012.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 07/25/2012] [Accepted: 07/30/2012] [Indexed: 05/11/2023]
Abstract
Plant tissues commonly undergo morphogenesis within a single tissue layer or between associated cells of the same tissue type such as vascular cells. Tissue morphogenesis may rely on an underlying tissue polarity marked by coordinated unidirectional asymmetric localisation of molecules to ends of cells. When observed in the plane of the tissue layer this is referred to as planar polarity and planar morphogenesis. However, planar morphogenesis can also involve multidirectional or differential growth of cells relying on cell-cell communication. Here, we review recent progress towards an understanding of hormonal coordination and molecular mechanisms underlying planar and tissue polarity as well as planar morphogenesis. Furthermore, we discuss the role of physical forces in planar morphogenesis and the contribution of tissue polarity to plant organ shape.
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Affiliation(s)
- Moritaka Nakamura
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden
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49
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Adam T, Bouhidel K, Der C, Robert F, Najid A, Simon-Plas F, Leborgne-Castel N. Constitutive expression of clathrin hub hinders elicitor-induced clathrin-mediated endocytosis and defense gene expression in plant cells. FEBS Lett 2012; 586:3293-8. [PMID: 22796492 DOI: 10.1016/j.febslet.2012.06.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
Abstract
Endocytosis has been recently implicated in the signaling network associated with the recognition of microbes by plants. In a previous study, we showed that the elicitor cryptogein was able to induce clathrin-mediated endocytosis (CME) in tobacco suspension cells. Herein, we investigate further the induced CME by means of a GFP-tagged clathrin light chain and a CME inhibitor, the hub domain of clathrin heavy chain. Hub constitutive expression does affect neither cell growth nor constitutive endocytosis but abolishes cryptogein-induced CME. Such an inhibition has no impact on early events in the cryptogein signaling pathway but reduces the expression of defense-associated genes.
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Affiliation(s)
- T Adam
- UMR Agroécologie 1347, AgroSup/INRA/Université de Bourgogne, Pôle Interaction Plantes Microorganismes, ERL6300 CNRS, Dijon, France
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50
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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