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Wiśniewska J, Kęsy J, Mucha N, Tyburski J. Auxin resistant 1 gene (AUX1) mediates auxin effect on Arabidopsis thaliana callus growth by regulating its content and distribution pattern. JOURNAL OF PLANT PHYSIOLOGY 2024; 293:154168. [PMID: 38176282 DOI: 10.1016/j.jplph.2023.154168] [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: 10/08/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Callus sustained growth relies heavily on auxin, which is supplied to the culture medium. Surprisingly, there is a noticeable absence of information regarding the involvement of carrier-mediated auxin polar transport gene in callus growth regulation. Here, we delve into the role of the AUXIN RESISTANT 1 (AUX1) influx transporter in the regulation of callus growth, comparing the effects under conditions of light versus darkness. It was observed that callus growth was significantly enhanced under light illumination. This growth-stimulatory effect was accompanied by a decrease in the levels of free auxin within the callus cells when compared to conditions of darkness. In the aux1-22 mutant callus, which lacks functional AUX1, there was a substantial reduction in IAA levels. Nonetheless, the mutant callus exhibited markedly higher growth rates compared to the wild type. This suggests that the reduction in exogenous auxin uptake through the AUX1-dependent pathway may prevent the overaccumulation of growth-restricting hormone concentrations. The growth-stimulatory effect of AUX1 deficiency was counteracted by nonspecific auxin influx transport inhibitors. This finding shows that other auxin influx carriers likely play a role in facilitating the diffusion of auxin from the culture medium to sustain high growth rates. AUX1 was primarily localized in the plasma membranes of the two outermost cell layers of the callus clump and the parenchyma cells adjacent to tracheary elements. Significantly, these locations coincided with the regions of maximal auxin concentration. Consequently, it can be inferred that AUX1 mediates the auxin distribution within the callus.
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Affiliation(s)
- Justyna Wiśniewska
- Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Jacek Kęsy
- Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Natalia Mucha
- Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Jarosław Tyburski
- Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland.
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Ménard D, Serk H, Decou R, Pesquet E. Inducible Pluripotent Suspension Cell Cultures (iPSCs) to Study Plant Cell Differentiation. Methods Mol Biol 2024; 2722:171-200. [PMID: 37897608 DOI: 10.1007/978-1-0716-3477-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
Inducing the differentiation of specific cell type(s) synchronously and on-demand is a great experimental system to understand the sequential progression of the cellular processes, their timing and their resulting properties for distinct isolated plant cells independently of their tissue context. The inducible differentiation in cell suspension cultures, moreover, enables to obtain large quantities of distinct cell types at specific development stage, which is not possible when using whole plants. The differentiation of tracheary elements (TEs) - the cell type responsible for the hydro-mineral sap conduction and skeletal support of plants in xylem tissues - has been the most studied using inducible cell suspension cultures. We herein describe how to establish and use inducible pluripotent suspension cell cultures (iPSCs) in Arabidopsis thaliana to trigger on-demand different cell types, such as TEs or mesophyll cells. We, moreover, describe the methods to establish, monitor, and modify the sequence, duration, and properties of differentiated cells using iPSCs.
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Affiliation(s)
- Delphine Ménard
- Department of Ecology, Environment and Plant Sciences (DEEP), Stockholm University, Stockholm, Sweden
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Henrik Serk
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Raphael Decou
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Edouard Pesquet
- Department of Ecology, Environment and Plant Sciences (DEEP), Stockholm University, Stockholm, Sweden.
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden.
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden.
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Han K, Zhao Y, Sun Y, Li Y. NACs, generalist in plant life. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2433-2457. [PMID: 37623750 PMCID: PMC10651149 DOI: 10.1111/pbi.14161] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.
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Affiliation(s)
- Kunjin Han
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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Kułak K, Wojciechowska N, Samelak-Czajka A, Jackowiak P, Bagniewska-Zadworna A. How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis. PLANT METHODS 2023; 19:129. [PMID: 37981669 PMCID: PMC10659056 DOI: 10.1186/s13007-023-01109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.
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Affiliation(s)
- Karolina Kułak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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Kim MH, Cho JS, Tran TNA, Nguyen TTT, Park EJ, Im JH, Han KH, Lee H, Ko JH. Comparative functional analysis of PdeNAC2 and AtVND6 in the tracheary element formation. TREE PHYSIOLOGY 2023:tpad042. [PMID: 37014763 DOI: 10.1093/treephys/tpad042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Tracheary elements (i.e., vessel elements and tracheids) are highly specialized, non-living cells present in the water-conducting xylem tissue. In angiosperms, proteins in the VASCULAR-RELATED NAC-DOMAIN (VND) subgroup of the NAC transcription factor family (e.g., AtVND6) are required for the differentiation of vessel elements through transcriptional regulation of genes responsible for secondary cell wall (SCW) formation and programmed cell death (PCD). Gymnosperms, however, produce only tracheids, the mechanism of which remains elusive. Here, we report functional characteristics of PdeNAC2, a VND homolog in Pinus densiflora, as a key regulator of tracheid formation. Interestingly, our molecular genetic analyses show that PdeNAC2 can induce the formation of vessel element-like cells in angiosperm plants, demonstrated by transgenic overexpression of either native or NAC domain-swapped synthetic genes of PdeNAC2 and AtVND6 in both Arabidopsis and hybrid poplar. Subsequently, genome-wide identification of direct target genes of PdeNAC2 and AtVND6 revealed 138 and 174 genes as putative direct targets, respectively, but only 17 genes were identified as common direct targets. Further analyses have found that PdeNAC2 does not control some AtVND6-dependent vessel differentiation genes in angiosperm plants, such as AtVRLK1, LBD15/30, and pit-forming ROP signaling genes. Collectively, our results suggest that different target gene repertoires of PdeNAC2 and AtVND6 may contribute to the evolution of tracheary elements.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Thi Ngoc Anh Tran
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Thi Thu Tram Nguyen
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Forest Bioresources Department, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Jong-Hee Im
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Kyung-Hwan Han
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
| | - Hyoshin Lee
- Forest Bioresources Department, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Republic of Korea
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Groover A. New surprises from tree vascular systems. A commentary on: 'Seasonal patterns of increases in stem girth, vessel development and hydraulic function in deciduous tree species'. ANNALS OF BOTANY 2022; 130:xii-xiv. [PMID: 35716061 PMCID: PMC9486879 DOI: 10.1093/aob/mcac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article comments on: Jessica Valdovinos-Ayala, Catherine Robles, Jaycie C. Fickle, Gonzalo Pérez-de-Lis, R. Brandon Pratt and Anna L. Jacobsen, Seasonal patterns of increases in stem girth, vessel development, and hydraulic function in deciduous tree species, Annals of Botany, Volume 130, Issue 3, 1 September 2022, Pages 355–365 https://doi.org/10.1093/aob/mcac032
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Xu H, Giannetti A, Sugiyama Y, Zheng W, Schneider R, Watanabe Y, Oda Y, Persson S. Secondary cell wall patterning-connecting the dots, pits and helices. Open Biol 2022; 12:210208. [PMID: 35506204 PMCID: PMC9065968 DOI: 10.1098/rsob.210208] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/07/2022] [Indexed: 01/04/2023] Open
Abstract
All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field.
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Affiliation(s)
- Huizhen Xu
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alessandro Giannetti
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Yuki Sugiyama
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Wenna Zheng
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - René Schneider
- Institute of Biochemistry and Biology, Plant Physiology Department, University of Potsdam, 14476 Potsdam, Germany
| | - Yoichiro Watanabe
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Staffan Persson
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Kamon E, Noda C, Higaki T, Demura T, Ohtani M. Calcium signaling contributes to xylem vessel cell differentiation via post-transcriptional regulation of VND7 downstream events. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:331-337. [PMID: 34782820 PMCID: PMC8562575 DOI: 10.5511/plantbiotechnology.21.0519a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Secondary cell walls (SCWs) accumulate in specific cell types of vascular plants, notably xylem vessel cells. Previous work has shown that calcium ions (Ca2+) participate in xylem vessel cell differentiation, but whether they function in SCW deposition remains unclear. In this study, we examined the role of Ca2+ in SCW deposition during xylem vessel cell differentiation using Arabidopsis thaliana suspension-cultured cells carrying the VND7-inducible system, in which VND7 activity can be post-translationally upregulated to induce transdifferentiation into protoxylem-type vessel cells. We observed that extracellular Ca2+ concentration was a crucial determinant of differentiation, although it did not have consistent effects on the transcription of VND7-downstream genes as a whole. Increasing the Ca2+ concentration reduced differentiation but the cells could generate the spiral patterning of SCWs. Exposure to a calcium-channel inhibitor partly restored differentiation but resulted in abnormal branched and net-like SCW patterning. These data suggest that Ca2+ signaling participates in xylem vessel cell differentiation via post-transcriptional regulation of VND7-downstream events, such as patterning of SCW deposition.
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Affiliation(s)
- Eri Kamon
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Chihiro Noda
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takumi Higaki
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto, Kumamoto 860-8555, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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Kim MH, Tran TNA, Cho JS, Park EJ, Lee H, Kim DG, Hwang S, Ko JH. Wood transcriptome analysis of Pinus densiflora identifies genes critical for secondary cell wall formation and NAC transcription factors involved in tracheid formation. TREE PHYSIOLOGY 2021; 41:1289-1305. [PMID: 33440425 DOI: 10.1093/treephys/tpab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 05/27/2023]
Abstract
Although conifers have significant ecological and economic value, information on transcriptional regulation of wood formation in conifers is still limited. Here, to gain insight into secondary cell wall (SCW) biosynthesis and tracheid formation in conifers, we performed wood tissue-specific transcriptome analyses of Pinus densiflora (Korean red pine) using RNA sequencing. In addition, to obtain full-length transcriptome information, PacBio single molecule real-time iso-sequencing was carried out using RNAs from 28 tissues of P. densiflora. Subsequent comparative tissue-specific transcriptome analysis successfully pinpointed critical genes encoding key proteins involved in biosynthesis of the major secondary wall components (cellulose, galactoglucomannan, xylan and lignin). Furthermore, we predicted a total of 62 NAC (NAM, ATAF1/2 and CUC2) family transcription factor members and identified seven PdeNAC genes preferentially expressed in developing xylem tissues in P. densiflora. Protoplast-based transcriptional activation analysis found that four PdeNAC genes, homologous to VND, NST and SND/ANAC075, upregulated GUS activity driven by an SCW-specific cellulose synthase promoter. Consistently, transient overexpression of the four PdeNACs induced xylem vessel cell-like SCW deposition in both tobacco (Nicotiana benthamiana) and Arabidopsis leaves. Taken together, our data provide a foundation for further research to unravel transcriptional regulation of wood formation in conifers, especially SCW formation and tracheid differentiation.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Thi Ngoc Anh Tran
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Hyoshin Lee
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Dong-Gwan Kim
- Department of Bioindustry and Bioresource Engineering, Department of Molecular Biology and Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Seoul 05006, Republic of Korea
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Department of Molecular Biology and Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Seoul 05006, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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Terada S, Kubo M, Akiyoshi N, Sano R, Nomura T, Sawa S, Ohtani M, Demura T. Expression of peat moss VASCULAR RELATED NAC-DOMAIN homologs in Nicotiana benthamiana leaf cells induces ectopic secondary wall formation. PLANT MOLECULAR BIOLOGY 2021; 106:309-317. [PMID: 33881701 DOI: 10.1007/s11103-021-01148-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE The homologs of VASCULAR RELATED NAC-DOMAIN in the peat moss Sphagnum palustre were identified and these transcriptional activity as the VNS family was conserved. In angiosperms, xylem vessel element differentiation is governed by the master regulators VASCULAR RELATED NAC-DOMAIN6 (VND6) and VND7, encoding plant-specific NAC transcription factors. Although vessel elements have not been found in bryophytes, differentiation of the water-conducting hydroid cells in the moss Physcomitrella patens is regulated by VND homologs termed VND-NST-SOMBRERO (VNS) genes. VNS genes are conserved in the land plant lineage, but their functions have not been elucidated outside of angiosperms and P. patens. The peat moss Sphagnum palustre, of class Sphagnopsida in the phylum Bryophyta, does not have hydroids and instead uses hyaline cells with thickened, helical-patterned cell walls and pores to store water in the leaves. Here, we performed whole-transcriptome analysis and de novo assembly using next generation sequencing in S. palustre, obtaining sequences for 68,305 genes. Among them, we identified seven VNS-like genes, SpVNS1-A, SpVNS1-B, SpVNS2-A, SpVNS2-B, SpVNS3-A, SpVNS3-B, and SpVNS4-A. Transient expression of these VNS-like genes, with the exception of SpVNS2-A, in Nicotiana benthamiana leaf cells resulted in ectopic thickening of secondary walls. This result suggests that the transcriptional activity observed in other VNS family members is functionally conserved in the VNS homologs of S. palustre.
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Affiliation(s)
- Shiori Terada
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Minoru Kubo
- Institute for Research Initiative, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan.
| | - Nobuhiro Akiyoshi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Baton Zone Program, Yokohama, Kanagawa, 230-0045, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.
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Zheng L, Yang J, Chen Y, Ding L, Wei J, Wang H. An improved and efficient method of Agrobacterium syringe infiltration for transient transformation and its application in the elucidation of gene function in poplar. BMC PLANT BIOLOGY 2021; 21:54. [PMID: 33478390 PMCID: PMC7818742 DOI: 10.1186/s12870-021-02833-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 01/11/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Forest trees have important economic and ecological value. As a model tree, poplar has played a significant role in elucidating the molecular mechanisms underlying tree biology. However, a lack of mutant libraries and time-consuming stable genetic transformation processes severely limit progress into the functional characterization of poplar genes. A convenient and fast transient transformation method is therefore needed to enhance progress on functional genomics in poplar. METHODS A total of 11 poplar clones were screened for amenability to syringe infiltration. Syringe infiltration was performed on the lower side of the leaves of young soil-grown plants. Transient expression was evaluated by visualizing the reporters β-glucuronidase (GUS) and green fluorescent protein (GFP). The experimental parameters of the syringe agroinfiltration were optimized based on the expression levels of the reporter luciferase (LUC). Stably transformed plants were regenerated from transiently transformed leaf explants through callus-induced organogenesis. The functions of Populus genes in secondary cell wall-thickening were characterized by visualizing lignin deposition therein after staining with basic fuchsin. RESULTS We greatly improved the transient transformation efficiency of syringe Agrobacterium infiltration in poplar through screening for a suitable poplar clone from a variety of clones and optimizing the syringe infiltration procedure. The selected poplar clone, Populus davidiana × P. bolleana, is amenable to Agrobacterium syringe infiltration, as indicated by the easy diffusion of the bacterial suspension inside the leaf tissues. Using this technique, we localized a variety of poplar proteins in specific intracellular organelles and illustrated the protein-protein and protein-DNA interactions. The transiently transformed leaves could be used to generate stably transformed plants with high efficiency through callus induction and differentiation processes. Furthermore, transdifferentiation of the protoxylem-like vessel element and ectopic secondary wall thickening were induced in the agroinfiltrated leaves via the transient overexpression of genes associated with secondary wall formation. CONCLUSIONS The application of P. davidiana × P. bolleana in Agrobacterium syringe infiltration provides a foundation for the rapid and high-throughput functional characterization of Populus genes in intact poplar plants, including those involved in wood formation, and provides an effective alternative to Populus stable genetic transformation.
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Affiliation(s)
- Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Jixiu Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
- College of Bioscience and Resources Environment, Beijing University of Agriculture, No. 7, Beinong Road, Huilongguan, Changping District, Beijing, 102206, People's Republic of China
| | - Yajuan Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Liping Ding
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China.
| | - Hongzhi Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China.
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12
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Iqbal MM, Hurgobin B, Holme AL, Appels R, Kaur P. Status and Potential of Single‐Cell Transcriptomics for Understanding Plant Development and Functional Biology. Cytometry A 2020; 97:997-1006. [DOI: 10.1002/cyto.a.24196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/08/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Muhammad Munir Iqbal
- UWA School of Agriculture and Environment, Faculty of Science The University of Western Australia 35 Stirling Hwy Perth WA 6009 Australia
- Genome Innovation Hub Telethon Kids Institute, Perth Children Hospital Nedlands WA 6009 Australia
| | - Bhavna Hurgobin
- School of Life Sciences, La Trobe University Bundoora Victoria 3086 Australia
| | - Andrea Lisa Holme
- Iain Fraser Cytometry Centre, IFCC Institute of Medical Sciences (IMS), School of Medicine, Medical Sciences and Nutrition University of Aberdeen Forester Hill Aberdeen AB25 2ZD UK
| | - Rudi Appels
- School of BioSciences, The University of Melbourne Victoria 3010 Australia
- School of Applied Biology, La Trobe University Bundoora Victoria 3086 Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, Faculty of Science The University of Western Australia 35 Stirling Hwy Perth WA 6009 Australia
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13
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Necrotic upper tips1 mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize. Proc Natl Acad Sci U S A 2020; 117:20908-20919. [PMID: 32778598 DOI: 10.1073/pnas.2005014117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Maintaining sufficient water transport during flowering is essential for proper organ growth, fertilization, and yield. Water deficits that coincide with flowering result in leaf wilting, necrosis, tassel browning, and sterility, a stress condition known as "tassel blasting." We identified a mutant, necrotic upper tips1 (nut1), that mimics tassel blasting and drought stress and reveals the genetic mechanisms underlying these processes. The nut1 phenotype is evident only after the floral transition, and the mutants have difficulty moving water as shown by dye uptake and movement assays. These defects are correlated with reduced protoxylem vessel thickness that indirectly affects metaxylem cell wall integrity and function in the mutant. nut1 is caused by an Ac transposon insertion into the coding region of a unique NAC transcription factor within the VND clade of Arabidopsis NUT1 localizes to the developing protoxylem of root, stem, and leaf sheath, but not metaxylem, and its expression is induced by flowering. NUT1 downstream target genes function in cell wall biosynthesis, apoptosis, and maintenance of xylem cell wall thickness and strength. These results show that maintaining protoxylem vessel integrity during periods of high water movement requires the expression of specialized, dynamically regulated transcription factors within the vasculature.
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14
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Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea. Int J Mol Sci 2020; 21:ijms21165706. [PMID: 32784897 PMCID: PMC7461206 DOI: 10.3390/ijms21165706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/01/2020] [Accepted: 08/06/2020] [Indexed: 01/13/2023] Open
Abstract
Plant polygalacturonases (PGs) are closely related to cell-separation events during plant growth and development by degrading pectin. Identifying and investigating their diversification of evolution and expression could shed light on research on their function. We conducted sequence, molecular evolution, and gene expression analyses of PG genes in Brassica oleracea. Ninety-nine B. oleracea PGs (BoPGs) were identified and divided into seven clades through phylogenetic analysis. The exon/intron structures and motifs were conserved within, but divergent between, clades. The second conserved domain (GDDC) may be more closely related to the identification of PGs. There were at least 79 common ancestor PGs between Arabidopsis thaliana and B. oleracea. The event of whole genome triplication and tandem duplication played important roles in the rapid expansion of the BoPG gene family, and gene loss may be an important mechanism in the generation of the diversity of BoPGs. By evaluating the expression in five tissues, we found that most of the expressed BoPGs in clades A, B, and E showed ubiquitous expression characteristics, and the expressed BoPGs in clades C, D, and F were mainly responsible for reproduction development. Most of the paralogous gene pairs (76.2%) exhibited divergent expression patterns, indicating that they may have experienced neofunctionalization or subfunctionalization. The cis-elements analysis showed that up to 96 BoPGs contained the hormone response elements in their promoters. In conclusion, our comparative analysis may provide a valuable data foundation for the further functional analysis of BoPGs during the development of B. oleracea.
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15
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Akiyoshi N, Nakano Y, Sano R, Kunigita Y, Ohtani M, Demura T. Involvement of VNS NAC-domain transcription factors in tracheid formation in Pinus taeda. TREE PHYSIOLOGY 2020; 40:704-716. [PMID: 31821470 DOI: 10.1093/treephys/tpz106] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/22/2019] [Accepted: 09/24/2019] [Indexed: 05/19/2023]
Abstract
Vascular plants have two types of water-conducting cells, xylem vessel cells (in angiosperms) and tracheid cells (in ferns and gymnosperms). These cells are commonly characterized by secondary cell wall (SCW) formation and programmed cell death (PCD), which increase the efficiency of water conduction. The differentiation of xylem vessel cells is regulated by a set of NAC (NAM, ATAF1/2 and CUC2) transcription factors, called the VASCULAR-RELATED NAC-DOMAIN (VND) family, in Arabidopsis thaliana Linne. The VNDs regulate the transcriptional induction of genes required for SCW formation and PCD. However, information on the transcriptional regulation of tracheid cell differentiation is still limited. Here, we performed functional analysis of loblolly pine (Pinus taeda Linne) VND homologs (PtaVNS, for VND, NST/SND, SMB-related protein). We identified five PtaVNS genes in the loblolly pine genome, and four of these PtaVNS genes were highly expressed in tissues with tracheid cells, such as shoot apices and developing xylem. Transient overexpression of PtaVNS genes induced xylem vessel cell-like patterning of SCW deposition in tobacco (Nicotiana benthamiana Domin) leaves, and up-regulated the promoter activities of loblolly pine genes homologous to SCW-related MYB transcription factor genes and cellulose synthase genes, as well as to cysteine protease genes for PCD. Collectively, our data indicated that PtaVNS proteins possess transcriptional activity to induce the molecular programs required for tracheid formation, i.e., SCW formation and PCD. Moreover, these findings suggest that the VNS-MYB-based transcriptional network regulating water-conducting cell differentiation in angiosperm and moss plants is conserved in gymnosperms.
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Affiliation(s)
- Nobuhiro Akiyoshi
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoshimi Nakano
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yusuke Kunigita
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content. Proc Natl Acad Sci U S A 2020; 117:3281-3290. [PMID: 31974310 PMCID: PMC7022211 DOI: 10.1073/pnas.1914422117] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
There is considerable interest in engineering plant cell wall components, particularly lignin, to improve forage quality and biomass properties for processing to fuels and bioproducts. However, modifying lignin content and/or composition in transgenic plants through down-regulation of lignin biosynthetic enzymes can induce expression of defense response genes in the absence of biotic or abiotic stress. Arabidopsis thaliana lines with altered lignin through down-regulation of hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) or loss of function of cinnamoyl CoA reductase 1 (CCR1) express a suite of pathogenesis-related (PR) protein genes. The plants also exhibit extensive cell wall remodeling associated with induction of multiple cell wall-degrading enzymes, a process which renders the corresponding biomass a substrate for growth of the cellulolytic thermophile Caldicellulosiruptor bescii lacking a functional pectinase gene cluster. The cell wall remodeling also results in the release of size- and charge-heterogeneous pectic oligosaccharide elicitors of PR gene expression. Genetic analysis shows that both in planta PR gene expression and release of elicitors are the result of ectopic expression in xylem of the gene ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1), which is normally expressed during anther and silique dehiscence. These data highlight the importance of pectin in cell wall integrity and the value of lignin modification as a tool to interrogate the informational content of plant cell walls.
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17
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Kaga Y, Yokoyama R, Sano R, Ohtani M, Demura T, Kuroha T, Shinohara N, Nishitani K. Interspecific Signaling Between the Parasitic Plant and the Host Plants Regulate Xylem Vessel Cell Differentiation in Haustoria of Cuscuta campestris. FRONTIERS IN PLANT SCIENCE 2020; 11:193. [PMID: 32231674 PMCID: PMC7082356 DOI: 10.3389/fpls.2020.00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/10/2020] [Indexed: 05/13/2023]
Abstract
The genus Cuscuta is stem parasitic angiosperms that parasitize a wide range of vascular plants via de novo formation of a distinctive parasitic organ called a haustorium. In the developing haustorium, meristematic cells, which are initiated from the stem cortical tissue, differentiate into haustorial parenchyma cells, which elongate, penetrate into the host tissues, and finally connect with the host vasculature. This interspecific vasculature connection allows the parasite to uptake water and nutrients from the host plant. Although histological aspects of haustorium development have been studied extensively, the molecular mechanisms underlying vasculature development and the interspecific connection with the host vasculature remain largely unknown. To gain insights into the interspecific cell-to-cell interactions involved in haustorium development, we established an in vitro haustorium induction system for Cuscuta campestris using Arabidopsis thaliana rosette leaves as the host plant tissue. The in vitro induction system was used to show that interaction with host tissue was required for the differentiation of parasite haustorial cells into xylem vessel cells. To further characterize the molecular events occurring during host-dependent xylem vessel cell differentiation in C. campestris, we performed a transcriptome analysis using samples from the in vitro induction system. The results showed that orthologs of genes involved in development and proliferation of vascular stem cells were up-regulated even in the absence of host tissue, whereas orthologs of genes required for xylem vessel cell differentiation were up-regulated only after some haustorial cells had elongated and contacted the host xylem. Consistent results were obtained by another transcriptome analysis of the haustorium development in C. campestris undergoing parasitization of an intact host plant. These findings suggest the involvement of host-derived signals in the regulation of non-autonomous xylem vessel differentiation and suggest that its connection to the host xylem during the haustorium development activates a set of key genes for differentiation into xylem vessel cells.
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Affiliation(s)
- Yuki Kaga
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryusuke Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Takeshi Kuroha
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Naoki Shinohara
- Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Kazuhiko Nishitani
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
- *Correspondence: Kazuhiko Nishitani,
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18
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Kärkönen A, Santanen A, Iwamoto K, Fukuda H. Plant Tissue Cultures. Methods Mol Biol 2020; 2149:89-109. [PMID: 32617931 DOI: 10.1007/978-1-0716-0621-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Plant tissue cultures are an efficient system to study cell wall biosynthesis in living cells in vivo. Tissue cultures also provide cells and culture medium from which enzymes and cell wall polymers can easily be separated for further studies. Tissue cultures with tracheary element differentiation or extracellular lignin formation have provided useful information related to several aspects of xylem and lignin formation. In this chapter, methods for nutrient medium preparation and callus culture initiation and its maintenance as well as those for protoplast isolation and viability observation are described. As a case study, we describe the establishment of a xylogenic culture of Zinnia elegans mesophyll cells.
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Affiliation(s)
- Anna Kärkönen
- Natural Resources Institute Finland (Luke), Production Systems, Plant Genetics, Helsinki, Finland.
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - Arja Santanen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kuninori Iwamoto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
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19
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Yang Y, Yoo CG, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Pu Y, Ragauskas AJ, Tuskan GA, Chen JG. PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biosynthesis and composition in Populus. BMC PLANT BIOLOGY 2019; 19:486. [PMID: 31711424 PMCID: PMC6849256 DOI: 10.1186/s12870-019-2111-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials production. Arabidopsis VASCULAR-RELATED NAC DOMAIN (VND) has been demonstrated to be a key transcription factor regulating secondary cell wall biosynthesis. However, less is known about its role in the woody species. RESULTS Here we report the functional characterization of Populus deltoides WOOD-ASSOCIATED NAC DOMAIN protein 3 (PdWND3A), a sequence homolog of Arabidopsis VND4 and VND5 that are members of transcription factor networks regulating secondary cell wall biosynthesis. PdWND3A was expressed at higher level in the xylem than in other tissues. The stem tissues of transgenic P. deltoides overexpressing PdWND3A (OXPdWND3A) contained more vessel cells than that of wild-type plants. Furthermore, lignin content and lignin monomer syringyl and guaiacyl (S/G) ratio were higher in OXPdWND3A transgenic plants than in wild-type plants. Consistent with these observations, the expression of FERULATE 5-HYDROXYLASE1 (F5H1), encoding an enzyme involved in the biosynthesis of sinapyl alcohol (S unit monolignol), was elevated in OXPdWND3A transgenic plants. Saccharification analysis indicated that the rate of sugar release was reduced in the transgenic plants. In addition, OXPdWND3A transgenic plants produced lower amounts of biomass than wild-type plants. CONCLUSIONS PdWND3A affects lignin biosynthesis and composition and negatively impacts sugar release and biomass production.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | | | | | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering & Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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20
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Tamura T, Endo H, Suzuki A, Sato Y, Kato K, Ohtani M, Yamaguchi M, Demura T. Affinity-based high-resolution analysis of DNA binding by VASCULAR-RELATED NAC-DOMAIN7 via fluorescence correlation spectroscopy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:298-313. [PMID: 31313414 DOI: 10.1111/tpj.14443] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
VASCULAR-RELATED NAC-DOMAIN7 (VND7) is the master transcription factor for vessel element differentiation in Arabidopsis thaliana. To identify the cis-acting sequence(s) bound by VND7, we employed fluorescence correlation spectroscopy (FCS) to find VND7-DNA interactions quantitatively. This identified an 18-bp sequence from the promoter of XYLEM CYSTEINE PEPTIDASE1 (XCP1), a direct target of VND7. A quantitative assay for binding affinity between VND7 and the 18-bp sequence revealed the core nucleotides contributing to specific binding between VND7 and the 18-bp sequence. Moreover, by combining the systematic evolution of ligands by exponential enrichment (SELEX) technique with known consensus sequences, we defined a motif termed the Ideal Core Structure for binding by VND7 (ICSV). We also used FCS to search for VND7 binding sequences in the promoter regions of other direct targets. Taking these data together, we proposed that VND7 preferentially binds to the ICSV sequence. Additionally, we found that substitutions among the core nucleotides affected transcriptional regulation by VND7 in vivo, indicating that the core nucleotides contribute to vessel-element-specific gene expression. Furthermore, our results demonstrate that FCS is a powerful tool for unveiling the DNA-binding properties of transcription factors.
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Affiliation(s)
- Taizo Tamura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Atsunobu Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yutaka Sato
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ko Kato
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama, 338-8570, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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21
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Rodriguez-Villalon A, Brady SM. Single cell RNA sequencing and its promise in reconstructing plant vascular cell lineages. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:47-56. [PMID: 31071514 DOI: 10.1016/j.pbi.2019.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
In the last decade, recent advances in single-cell RNA sequencing coupled with computational algorithms have opened new avenues to study the cell type composition of tissues and organs as well as to infer cell developmental trajectories. These technologies have been used to resolve and map atlases of tissues and organs in many animal species as well as to further order cell developmental trajectories. Despite these advances in animals, many of the current plant cell type expression profiles confound multiple developmental stages preventing an accurate monitoring of cell lineage. In this review, we propose how the application of single-cell sequencing will improve our molecular understanding of cell type differentiation. Using root vascular cells as a model, we highlight the potential of single cell transcriptomics as well as its limitations to monitor the progression of vascular maturation. By comparing cell morphology, functionality and gene expression, we aim to provide a new perspective of plant cell type differentiation.
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Affiliation(s)
| | - Siobhan M Brady
- Department of Plant Biology and the Genome Center, University of California, Davis, CA 95616, USA.
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Tikhomirova LI, Bazarnova NG, Sinitsyna AA. Histochemical Study of Xylem Cells in In Vitro Culture of Iris sibirica L. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162018070129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tan TT, Demura T, Ohtani M. Creating vessel elements in vitro: Towards a comprehensive understanding of the molecular basis of xylem vessel element differentiation. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:1-6. [PMID: 31275042 PMCID: PMC6566013 DOI: 10.5511/plantbiotechnology.18.1119b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 05/30/2023]
Abstract
Xylem is an essential conductive tissue in vascular plants, and secondary cell wall polymers found in xylem vessel elements, such as cellulose, hemicellulose, and lignin, are promising sustainable bioresources. Thus, understanding the molecular mechanisms underlying xylem vessel element differentiation is an important step towards increasing woody biomass and crop yields. Establishing in vitro induction systems, in which vessel element differentiation is induced by phytohormonal stimuli or by overexpression of specific transcription factors, has been vital to this research. In this review, we present an overview of these in vitro induction systems, and describe two recently developed in vitro induction systems, VISUAL (Vascular cell Induction culture System Using Arabidopsis Leaves) and the KDB system. Furthermore, we discuss the potentials and limitations of each of these new in vitro induction systems for advancing our understanding of the molecular mechanisms driving xylem vessel element differentiation.
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Affiliation(s)
- Tian Tian Tan
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - Taku Demura
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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Cubría-Radío M, Nowack MK. Transcriptional networks orchestrating programmed cell death during plant development. Curr Top Dev Biol 2018; 131:161-184. [PMID: 30612616 PMCID: PMC7116394 DOI: 10.1016/bs.ctdb.2018.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Transcriptional gene regulation is a fundamental biological principle in the development of eukaryotes. It does control not only cell proliferation, specification, and differentiation, but also cell death processes as an integral feature of an organism's developmental program. As in animals, developmentally regulated cell death in plants occurs in numerous contexts and is of vital importance for plant vegetative and reproductive development. In comparison with the information available on the molecular regulation of programmed cell death (PCD) in animals, however, our knowledge on plant PCD still remains scarce. Here, we discuss the functions of different classes of transcription factors that have been implicated in the control of developmentally regulated cell death. Though doubtlessly representing but a first layer of PCD regulation, information on PCD-regulating transcription factors and their targets represents a promising strategy to understand the complex machinery that ensures the precise and failsafe execution of PCD processes in plant development.
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Affiliation(s)
- Marta Cubría-Radío
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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25
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Takenaka Y, Watanabe Y, Schuetz M, Unda F, Hill JL, Phookaew P, Yoneda A, Mansfield SD, Samuels L, Ohtani M, Demura T. Patterned Deposition of Xylan and Lignin is Independent from that of the Secondary Wall Cellulose of Arabidopsis Xylem Vessels. THE PLANT CELL 2018; 30:2663-2676. [PMID: 30337427 PMCID: PMC6305973 DOI: 10.1105/tpc.18.00292] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/24/2018] [Accepted: 10/17/2018] [Indexed: 05/19/2023]
Abstract
The secondary cell wall (SCW) of xylem vessel cells provides rigidity and strength that enables efficient water conduction throughout the plant. To gain insight into SCW deposition, we mutagenized Arabidopsis thaliana VASCULAR-RELATED NAC-DOMAIN7-inducible plant lines, in which ectopic protoxylem vessel cell differentiation is synchronously induced. The baculites mutant was isolated based on the absence of helical SCW patterns in ectopically-induced protoxylem vessel cells, and mature baculites plants exhibited an irregular xylem (irx) mutant phenotype in mature plants. A single nucleic acid substitution in the CELLULOSE SYNTHASE SUBUNIT 7 (CESA7) gene in baculites was identified: while the mutation was predicted to produce a C-terminal truncated protein, immunoblot analysis revealed that cesa7bac mutation results in loss of production of CESA7 proteins, indicating that baculites is a novel cesa7 loss-of-function mutant. In cesa7bac , despite a lack of patterned cellulose deposition, the helically-patterned deposition of other SCW components, such as the hemicellulose xylan and the phenolic polymer lignin, was not affected. Similar phenotypes were found in another point mutation mutant cesa7mur10-2 , and an established knock-out mutant, cesa7irx3-4 Taken together, we propose that the spatio-temporal deposition of different SCW components, such as xylan and lignin, is not dependent on cellulose patterning.
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Affiliation(s)
- Yuto Takenaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yoichiro Watanabe
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada
| | - Mathias Schuetz
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Faride Unda
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada
| | - Joseph L Hill
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Pawittra Phookaew
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Arata Yoneda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada
| | - Lacey Samuels
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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26
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Noguchi M, Fujiwara M, Sano R, Nakano Y, Fukao Y, Ohtani M, Demura T. Proteomic analysis of xylem vessel cell differentiation in VND7-inducible tobacco BY-2 cells by two-dimensional gel electrophoresis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:31-37. [PMID: 31275035 PMCID: PMC6543734 DOI: 10.5511/plantbiotechnology.18.0129a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/29/2018] [Indexed: 05/09/2023]
Abstract
The xylem vessel is an essential structure for water conduction in vascular plants. Xylem vessel cells deposit thick secondary cell walls and undergo programmed cell death, to function as water-conducting elements. Since the discovery of the plant-specific NAC domain-type VASCULAR-RELATED NAC-DOMAIN (VND) transcription factors, which function as master switches of xylem vessel cell differentiation in Arabidopsis, much has been learned about the transcriptional regulatory network of xylem vessel cell differentiation. However, little is known about proteome dynamics during xylem vessel cell differentiation. Here, we performed two-dimensional electrophoresis-based proteomic analysis of xylem vessel cell differentiation using a transgenic tobacco BY-2 cell line carrying the VND7-inducible system (BY-2/35S::VND7-VP16-GR), in which synchronous trans-differentiation into xylem vessel cells can be induced by the application of a glucocorticoid. Of the 47 spots revealed by gel electrophoresis, we successfully identified 40 proteins. Seventeen proteins, including several well-characterized proteins such as a cysteine protease and serine carboxypeptidase (involved in programmed cell death), were upregulated after 24 h of induction. However, previous transcriptomic analysis showed that only eight of these proteins are upregulated at the transcriptional level during xylem vessel cell differentiation in BY-2/35S::VND7-VP16-GR cells. These findings suggest that post-transcriptional regulation strongly affects proteomic dynamics during xylem vessel cell differentiation.
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Affiliation(s)
- Masahiro Noguchi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Masayuki Fujiwara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ryosuke Sano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoshimi Nakano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoichiro Fukao
- College of Life Sciences, Department of Bioinformatics, Ritsumeikan University, Shiga 525-8577, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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27
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Endo S, Iwamoto K, Fukuda H. Overexpression and cosuppression of xylem-related genes in an early xylem differentiation stage-specific manner by the AtTED4 promoter. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:451-458. [PMID: 28664596 PMCID: PMC5787829 DOI: 10.1111/pbi.12784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/20/2017] [Accepted: 06/20/2017] [Indexed: 05/03/2023]
Abstract
Tissue-specific overexpression of useful genes, which we can design according to their cause-and-effect relationships, often gives valuable gain-of-function phenotypes. To develop genetic tools in woody biomass engineering, we produced a collection of Arabidopsis lines that possess chimeric genes of a promoter of an early xylem differentiation stage-specific gene, Arabidopsis Tracheary Element Differentiation-related 4 (AtTED4) and late xylem development-associated genes, many of which are uncharacterized. The AtTED4 promoter directed the expected expression of transgenes in developing vascular tissues from young to mature stage. Of T2 lines examined, 42%, 49% and 9% were judged as lines with the nonrepeat type insertion, the simple repeat type insertion and the other repeat type insertion of transgenes. In 174 T3 lines, overexpression lines were confirmed for 37 genes, whereas only cosuppression lines were produced for eight genes. The AtTED4 promoter activity was high enough to overexpress a wide range of genes over wild-type expression levels, even though the wild-type expression is much higher than AtTED4 expression for several genes. As a typical example, we investigated phenotypes of pAtTED4::At5g60490 plants, in which both overexpression and cosuppression lines were included. Overexpression but not cosuppression lines showed accelerated xylem development, suggesting the positive role of At5g60490 in xylem development. Taken together, this study provides valuable results about behaviours of various genes expressed under an early xylem-specific promoter and about usefulness of their lines as genetic tools in woody biomass engineering.
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Affiliation(s)
- Satoshi Endo
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Kuninori Iwamoto
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Hiroo Fukuda
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
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28
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Zhang J, Xie M, Tuskan GA, Muchero W, Chen JG. Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1535. [PMID: 30405670 PMCID: PMC6206300 DOI: 10.3389/fpls.2018.01535] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/28/2018] [Indexed: 05/19/2023]
Abstract
Plant cell walls provide structural support for growth and serve as a barrier for pathogen attack. Plant cell walls are also a source of renewable biomass for conversion to biofuels and bioproducts. Understanding plant cell wall biosynthesis and its regulation is of critical importance for the genetic modification of plant feedstocks for cost-effective biofuels and bioproducts conversion and production. Great progress has been made in identifying enzymes involved in plant cell wall biosynthesis, and in Arabidopsis it is generally recognized that the regulation of genes encoding these enzymes is under a transcriptional regulatory network with coherent feedforward and feedback loops. However, less is known about the transcriptional regulation of plant secondary cell wall (SCW) biosynthesis in woody species despite of its high relevance to biofuels and bioproducts conversion and production. In this article, we synthesize recent progress on the transcriptional regulation of SCW biosynthesis in Arabidopsis and contrast to what is known in woody species. Furthermore, we evaluate progress in related emerging regulatory machineries targeting transcription factors in this complex regulatory network of SCW biosynthesis.
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Affiliation(s)
- Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Wellington Muchero, Jin-Gui Chen,
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Wellington Muchero, Jin-Gui Chen,
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29
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Anand G, Yadav S, Tanveer A, Nasim J, Singh NK, Dubey AK, Yadav D. Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula, Sorghum bicolor, Vitis vinifera and Oryza sativa Using Comparative Genomics Approach. Interdiscip Sci 2017; 10:704-721. [PMID: 29243204 DOI: 10.1007/s12539-017-0230-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 02/03/2017] [Accepted: 04/01/2017] [Indexed: 11/24/2022]
Abstract
The polygalacturonases (PG) is one of the important members of pectin-degrading glycoside hydrolases of the family GH28. In plants, PG represents multigene families associated with diverse processes. In the present study, an attempt has been made to investigate the diversity of PG genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. The genome-wide assessment of Medicago truncatula, Vitis vinifera Sorghum bicolor, and Oryza sativa L. ssp. japonica genomes revealed 53, 49, 38 and 35 PG-like (PGL) genes, respectively. The predominance of glyco_hydro_28 domain, hydrophilic nature and genes with multiple introns were uniformly observed. The subcellular localization showed the presence of signal sequences targeting the secretory pathways. The phylogenetic tree constructed marked uniformity with three distinct clusters for each plant irrespective of the variability in the genome sizes. The site-specific selection pressure analysis based on K a/K s values showed predominance of purifying selection pressures among different groups identified in these plants. The functional divergence analysis revealed significant site-specific selective constraints. Results of site-specific selective pressure analysis throw light on the functional diversity of PGs in various plant processes and hence its constitutive nature. These findings are further strengthened by functional divergence analysis which reveals functionally diverse groups in all the four species representing monocots and dicots. The outcome of the present work could be utilized for deciphering the novel functions of PGs in plants.
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Affiliation(s)
- Gautam Anand
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India
| | - Sangeeta Yadav
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India
| | - Aiman Tanveer
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India
| | - Jeya Nasim
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India
| | - Nitish K Singh
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India.,Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Amit K Dubey
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India
| | - Dinesh Yadav
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India.
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30
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Affiliation(s)
- Raili Ruonala
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;, ,
| | - Donghwi Ko
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;, ,
| | - Ykä Helariutta
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;, ,
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31
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Schneider R, Tang L, Lampugnani ER, Barkwill S, Lathe R, Zhang Y, McFarlane HE, Pesquet E, Niittyla T, Mansfield SD, Zhou Y, Persson S. Two Complementary Mechanisms Underpin Cell Wall Patterning during Xylem Vessel Development. THE PLANT CELL 2017; 29:2433-2449. [PMID: 28947492 PMCID: PMC5774576 DOI: 10.1105/tpc.17.00309] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/29/2017] [Accepted: 09/24/2017] [Indexed: 05/02/2023]
Abstract
The evolution of the plant vasculature was essential for the emergence of terrestrial life. Xylem vessels are solute-transporting elements in the vasculature that possess secondary wall thickenings deposited in intricate patterns. Evenly dispersed microtubule (MT) bands support the formation of these wall thickenings, but how the MTs direct cell wall synthesis during this process remains largely unknown. Cellulose is the major secondary wall constituent and is synthesized by plasma membrane-localized cellulose synthases (CesAs) whose catalytic activity propels them through the membrane. We show that the protein CELLULOSE SYNTHASE INTERACTING1 (CSI1)/POM2 is necessary to align the secondary wall CesAs and MTs during the initial phase of xylem vessel development in Arabidopsis thaliana and rice (Oryza sativa). Surprisingly, these MT-driven patterns successively become imprinted and sufficient to sustain the continued progression of wall thickening in the absence of MTs and CSI1/POM2 function. Hence, two complementary principles underpin wall patterning during xylem vessel development.
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Affiliation(s)
- Rene Schneider
- School of Biosciences, University of Melbourne, Parkville 3010, Melbourne, Australia
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Lu Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Edwin R Lampugnani
- School of Biosciences, University of Melbourne, Parkville 3010, Melbourne, Australia
| | - Sarah Barkwill
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Rahul Lathe
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Yi Zhang
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Heather E McFarlane
- School of Biosciences, University of Melbourne, Parkville 3010, Melbourne, Australia
| | - Edouard Pesquet
- Arrhenius Laboratories, Department of Ecology, Environment and Plant Sciences (DEEP), Stockholm University, 160 91 Stockholm, Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Totte Niittyla
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville 3010, Melbourne, Australia
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
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32
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Ohashi T, Jinno J, Inoue Y, Ito S, Fujiyama K, Ishimizu T. A polygalacturonase localized in the Golgi apparatus in Pisum sativum. J Biochem 2017; 162:193-201. [PMID: 28338792 DOI: 10.1093/jb/mvx014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/30/2017] [Indexed: 11/13/2022] Open
Abstract
Pectin is a plant cell wall constituent that is mainly composed of polygalacturonic acid (PGA), a linear α1,4-d-galacturonic acid (GalUA) backbone. Polygalacturonase (PG) hydrolyzes the α1,4-linkages in PGA. Nearly all plant PGs identified thus far are secreted as soluble proteins. Here we describe the microsomal PG activity in pea (Pisum sativum) epicotyls and present biochemical evidence that it was localized to the Golgi apparatus, where pectins are biosynthesized. The microsomal PG was purified, and it was enzymatically characterized. The purified enzyme showed maximum activity towards pyridylaminated oligogalacturonic acids with six degrees of polymerization (PA-GalUA6), with a Km value of 11 μM for PA-GalUA6. The substrate preference of the enzyme was complementary to that of PGA synthase. The main PG activity in microsomes was detected in the Golgi fraction by sucrose density gradient ultracentrifugation. The activity of the microsomal PG was lower in rapidly growing epicotyls, in contrast to the high expression of PGA synthase. The role of this PG in the regulation of pectin biosynthesis or plant growth is discussed.
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Affiliation(s)
- Takao Ohashi
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Jun Jinno
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yoshiyuki Inoue
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shoko Ito
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takeshi Ishimizu
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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33
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MacMillan CP, Birke H, Chuah A, Brill E, Tsuji Y, Ralph J, Dennis ES, Llewellyn D, Pettolino FA. Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. BMC Genomics 2017; 18:539. [PMID: 28720072 PMCID: PMC5516393 DOI: 10.1186/s12864-017-3902-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre. RESULTS Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis. CONCLUSIONS Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotton stems are compositionally very different from that reported for other plant species, including Arabidopsis. The current definition of a 'typical' primary or secondary cell wall might not be applicable to all cell types in all plant species.
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Affiliation(s)
| | - Hannah Birke
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Aaron Chuah
- John Curtin School of Medical Research, The Australian National University, ACT, Canberra, 2601, Australia
| | - Elizabeth Brill
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia
| | - Yukiko Tsuji
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - John Ralph
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | | | - Danny Llewellyn
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia
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34
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Hacke UG, Spicer R, Schreiber SG, Plavcová L. An ecophysiological and developmental perspective on variation in vessel diameter. PLANT, CELL & ENVIRONMENT 2017; 40:831-845. [PMID: 27304704 DOI: 10.1111/pce.12777] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 05/05/2023]
Abstract
Variation in xylem vessel diameter is one of the most important parameters when evaluating plant water relations. This review provides a synthesis of the ecophysiological implications of variation in lumen diameter together with a summary of our current understanding of vessel development and its endogenous regulation. We analyzed inter-specific variation of the mean hydraulic vessel diameter (Dv ) across biomes, intra-specific variation of Dv under natural and controlled conditions, and intra-plant variation. We found that the Dv measured in young branches tends to stay below 30 µm in regions experiencing winter frost, whereas it is highly variable in the tropical rainforest. Within a plant, the widest vessels are often found in the trunk and in large roots; smaller diameters have been reported for leaves and small lateral roots. Dv varies in response to environmental factors and is not only a function of plant size. Despite the wealth of data on vessel diameter variation, the regulation of diameter is poorly understood. Polar auxin transport through the vascular cambium is a key regulator linking foliar and xylem development. Limited evidence suggests that auxin transport is also a determinant of vessel diameter. The role of auxin in cell expansion and in establishing longitudinal continuity during secondary growth deserve further study.
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Affiliation(s)
- Uwe G Hacke
- University of Alberta, Department of Renewable Resources, Edmonton, AB T6G 2E3, Canada
| | - Rachel Spicer
- Connecticut College, Department of Botany, New London, CT 06320, USA
| | - Stefan G Schreiber
- University of Alberta, Department of Renewable Resources, Edmonton, AB T6G 2E3, Canada
| | - Lenka Plavcová
- University of Hradec Králové, Department of Biology, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
- Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, 128 44, Czech Republic
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35
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Iakimova ET, Woltering EJ. Xylogenesis in zinnia (Zinnia elegans) cell cultures: unravelling the regulatory steps in a complex developmental programmed cell death event. PLANTA 2017; 245:681-705. [PMID: 28194564 PMCID: PMC5357506 DOI: 10.1007/s00425-017-2656-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 01/27/2017] [Indexed: 05/20/2023]
Abstract
MAIN CONCLUSION Physiological and molecular studies support the view that xylogenesis can largely be determined as a specific form of vacuolar programmed cell death (PCD). The studies in xylogenic zinnia cell culture have led to many breakthroughs in xylogenesis research and provided a background for investigations in other experimental models in vitro and in planta . This review discusses the most essential earlier and recent findings on the regulation of xylem elements differentiation and PCD in zinnia and other xylogenic systems. Xylogenesis (the formation of water conducting vascular tissue) is a paradigm of plant developmental PCD. The xylem vessels are composed of fused tracheary elements (TEs)-dead, hollow cells with patterned lignified secondary cell walls. They result from the differentiation of the procambium and cambium cells and undergo cell death to become functional post-mortem. The TE differentiation proceeds through a well-coordinated sequence of events in which differentiation and the programmed cellular demise are intimately connected. For years a classical experimental model for studies on xylogenesis was the xylogenic zinnia (Zinnia elegans) cell culture derived from leaf mesophyll cells that, upon induction by cytokinin and auxin, transdifferentiate into TEs. This cell system has been proven very efficient for investigations on the regulatory components of xylem differentiation which has led to many discoveries on the mechanisms of xylogenesis. The knowledge gained from this system has potentiated studies in other xylogenic cultures in vitro and in planta. The present review summarises the previous and latest findings on the hormonal and biochemical signalling, metabolic pathways and molecular and gene determinants underlying the regulation of xylem vessels differentiation in zinnia cell culture. Highlighted are breakthroughs achieved through the use of xylogenic systems from other species and newly introduced tools and analytical approaches to study the processes. The mutual dependence between PCD signalling and the differentiation cascade in the program of TE development is discussed.
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Affiliation(s)
| | - Ernst J Woltering
- Wageningen University and Research, Food and Biobased Research, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.
- Wageningen University, Horticulture and Product Physiology, P.O. Box 630, 6700 AP, Wageningen, The Netherlands.
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Wei Q, Jiao C, Guo L, Ding Y, Cao J, Feng J, Dong X, Mao L, Sun H, Yu F, Yang G, Shi P, Ren G, Fei Z. Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots. THE NEW PHYTOLOGIST 2017; 214:81-96. [PMID: 27859288 DOI: 10.1111/nph.14284] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/13/2016] [Indexed: 05/27/2023]
Abstract
The primary thickening growth of Moso (Phyllostachys edulis) underground shoots largely determines the culm circumference. However, its developmental mechanisms remain largely unknown. Using an integrated anatomy, mathematics and genomics approach, we systematically studied cellular and molecular mechanisms underlying the growth of Moso underground shoots. We discovered that the growth displayed a spiral pattern and pith played an important role in promoting the primary thickening process of Moso underground shoots and driving the evolution of culms with different sizes among different bamboo species. Different with model plants, the shoot apical meristem (SAM) of Moso is composed of six layers of cells. Comparative transcriptome analysis identified a large number of genes related to the vascular tissue formation that were significantly upregulated in a thick wall variant with narrow pith cavity, mildly spiral growth, and flat and enlarged SAM, including those related to plant hormones and those involved in cell wall development. These results provide a systematic perspective on the primary thickening growth of Moso underground shoots, and support a plausible mechanism resulting in the narrow pith cavity, weak spiral growth but increased vascular bundle of the thick wall Moso.
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Affiliation(s)
- Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Junjie Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Jianyuan Feng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Xiaobo Dong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Linyong Mao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, 330045, China
| | - Guangyao Yang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, 330045, China
| | - Peijian Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
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Xiao C, Barnes WJ, Zamil MS, Yi H, Puri VM, Anderson CT. Activation tagging of Arabidopsis POLYGALACTURONASE INVOLVED IN EXPANSION2 promotes hypocotyl elongation, leaf expansion, stem lignification, mechanical stiffening, and lodging. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1159-1173. [PMID: 28004869 DOI: 10.1111/tpj.13453] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/14/2016] [Accepted: 12/08/2016] [Indexed: 05/19/2023]
Abstract
Pectin is the most abundant component of primary cell walls in eudicot plants. The modification and degradation of pectin affects multiple processes during plant development, including cell expansion, organ initiation, and cell separation. However, the extent to which pectin degradation by polygalacturonases affects stem development and secondary wall formation remains unclear. Using an activation tag screen, we identified a transgenic Arabidopsis thaliana line with longer etiolated hypocotyls, which overexpresses a gene encoding a polygalacturonase. We designated this gene as POLYGALACTURONASE INVOLVED IN EXPANSION2 (PGX2), and the corresponding activation tagged line as PGX2AT . PGX2 is widely expressed in young seedlings and in roots, stems, leaves, flowers, and siliques of adult plants. PGX2-GFP localizes to the cell wall, and PGX2AT plants show higher total polygalacturonase activity and smaller pectin molecular masses than wild-type controls, supporting a function for this protein in apoplastic pectin degradation. A heterologously expressed, truncated version of PGX2 also displays polygalacturonase activity in vitro. Like previously identified PGX1AT plants, PGX2AT plants have longer hypocotyls and larger rosette leaves, but they also uniquely display early flowering, earlier stem lignification, and lodging stems with enhanced mechanical stiffness that is possibly due to decreased stem thickness. Together, these results indicate that PGX2 both functions in cell expansion and influences secondary wall formation, providing a possible link between these two developmental processes.
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Affiliation(s)
- Chaowen Xiao
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA
| | - William J Barnes
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA
| | - M Shafayet Zamil
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hojae Yi
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Virendra M Puri
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Charles T Anderson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA
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Ohtani M, Morisaki K, Sawada Y, Sano R, Uy ALT, Yamamoto A, Kurata T, Nakano Y, Suzuki S, Matsuda M, Hasunuma T, Hirai MY, Demura T. Primary Metabolism during Biosynthesis of Secondary Wall Polymers of Protoxylem Vessel Elements. PLANT PHYSIOLOGY 2016; 172:1612-1624. [PMID: 27600813 PMCID: PMC5100780 DOI: 10.1104/pp.16.01230] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/02/2016] [Indexed: 05/02/2023]
Abstract
Xylem vessels, the water-conducting cells in vascular plants, undergo characteristic secondary wall deposition and programmed cell death. These processes are regulated by the VASCULAR-RELATED NAC-DOMAIN (VND) transcription factors. Here, to identify changes in metabolism that occur during protoxylem vessel element differentiation, we subjected tobacco (Nicotiana tabacum) BY-2 suspension culture cells carrying an inducible VND7 system to liquid chromatography-mass spectrometry-based wide-target metabolome analysis and transcriptome analysis. Time-course data for 128 metabolites showed dynamic changes in metabolites related to amino acid biosynthesis. The concentration of glyceraldehyde 3-phosphate, an important intermediate of the glycolysis pathway, immediately decreased in the initial stages of cell differentiation. As cell differentiation progressed, specific amino acids accumulated, including the shikimate-related amino acids and the translocatable nitrogen-rich amino acid arginine. Transcriptome data indicated that cell differentiation involved the active up-regulation of genes encoding the enzymes catalyzing fructose 6-phosphate biosynthesis from glyceraldehyde 3-phosphate, phosphoenolpyruvate biosynthesis from oxaloacetate, and phenylalanine biosynthesis, which includes shikimate pathway enzymes. Concomitantly, active changes in the amount of fructose 6-phosphate and phosphoenolpyruvate were detected during cell differentiation. Taken together, our results show that protoxylem vessel element differentiation is associated with changes in primary metabolism, which could facilitate the production of polysaccharides and lignin monomers and, thus, promote the formation of the secondary cell wall. Also, these metabolic shifts correlate with the active transcriptional regulation of specific enzyme genes. Therefore, our observations indicate that primary metabolism is actively regulated during protoxylem vessel element differentiation to alter the cell's metabolic activity for the biosynthesis of secondary wall polymers.
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Affiliation(s)
- Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Keiko Morisaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Yuji Sawada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Ryosuke Sano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Abigail Loren Tung Uy
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Atsushi Yamamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Yoshimi Nakano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Shiro Suzuki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Mami Matsuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Tomohisa Hasunuma
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Masami Yokota Hirai
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.)
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.)
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.)
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (M.O., K.M., R.S., A.L.T.U., A.Y., T.K., Y.N., T.D.);
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan (T.K.);
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan (Y.N.);
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan (S.S.);
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada, Kobe 657-8501, Japan (M.M., T.H.); and
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.O., Y.S., M.Y.H., T.D.)
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Li Z, Omranian N, Neumetzler L, Wang T, Herter T, Usadel B, Demura T, Giavalisco P, Nikoloski Z, Persson S. A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis. PLANT PHYSIOLOGY 2016; 172:1334-1351. [PMID: 27566165 PMCID: PMC5047112 DOI: 10.1104/pp.16.01100] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/23/2016] [Indexed: 05/02/2023]
Abstract
Plant cell walls are essential for plant growth and development. The cell walls are traditionally divided into primary walls, which surround growing cells, and secondary walls, which provide structural support to certain cell types and promote their functions. While much information is available about the enzymes and components that contribute to the production of these two types of walls, much less is known about the transition from primary to secondary wall synthesis. To address this question, we made use of a transcription factor system in Arabidopsis (Arabidopsis thaliana) in which an overexpressed master secondary wall-inducing transcription factor, VASCULAR-RELATED NAC DOMAIN PROTEIN7, can be redirected into the nucleus by the addition of dexamethasone. We established the time frame during which primary wall synthesis changed into secondary wall production in dexamethasone-treated seedlings and measured transcript and metabolite abundance at eight time points after induction. Using cluster- and network-based analyses, we integrated the data sets to explore coordination between transcripts, metabolites, and the combination of the two across the time points. We provide the raw data as well as a range of network-based analyses. These data reveal links between hormone signaling and metabolic processes during the formation of secondary walls and provide a framework toward a deeper understanding of how primary walls transition into secondary walls.
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Affiliation(s)
- Zheng Li
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Nooshin Omranian
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Lutz Neumetzler
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Ting Wang
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Thomas Herter
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Bjoern Usadel
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Taku Demura
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Patrick Giavalisco
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Zoran Nikoloski
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Staffan Persson
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
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Rodríguez-Celma J, Ceballos-Laita L, Grusak MA, Abadía J, López-Millán AF. Plant fluid proteomics: Delving into the xylem sap, phloem sap and apoplastic fluid proteomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:991-1002. [PMID: 27033031 DOI: 10.1016/j.bbapap.2016.03.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 12/12/2022]
Abstract
The phloem sap, xylem sap and apoplastic fluid play key roles in long and short distance transport of signals and nutrients, and act as a barrier against local and systemic pathogen infection. Among other components, these plant fluids contain proteins which are likely to be important players in their functionalities. However, detailed information about their proteomes is only starting to arise due to the difficulties inherent to the collection methods. This review compiles the proteomic information available to date in these three plant fluids, and compares the proteomes obtained in different plant species in order to shed light into conserved functions in each plant fluid. Inter-species comparisons indicate that all these fluids contain the protein machinery for self-maintenance and defense, including proteins related to cell wall metabolism, pathogen defense, proteolysis, and redox response. These analyses also revealed that proteins may play more relevant roles in signaling in the phloem sap and apoplastic fluid than in the xylem sap. A comparison of the proteomes of the three fluids indicates that although functional categories are somewhat similar, proteins involved are likely to be fluid-specific, except for a small group of proteins present in the three fluids, which may have a universal role, especially in cell wall maintenance and defense. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Jorge Rodríguez-Celma
- University of East Anglia/John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Laura Ceballos-Laita
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 13034, E-50080 Zaragoza, Spain
| | - Michael A Grusak
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA
| | - Javier Abadía
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 13034, E-50080 Zaragoza, Spain
| | - Ana-Flor López-Millán
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 13034, E-50080 Zaragoza, Spain; USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA.
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Etchells JP, Smit ME, Gaudinier A, Williams CJ, Brady SM. A brief history of the TDIF-PXY signalling module: balancing meristem identity and differentiation during vascular development. THE NEW PHYTOLOGIST 2016; 209:474-84. [PMID: 26414535 DOI: 10.1111/nph.13642] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 08/11/2015] [Indexed: 05/25/2023]
Abstract
474 I. 474 II. 475 III. 475 IV. 477 V. 477 VI. 477 VII. 479 VIII. 481 482 References 482 SUMMARY: A significant proportion of terrestrial biomass is constituted of xylem cells that make up woody plant tissue. Xylem is required for water transport, and is present in the vascular tissue with a second conductive tissue, phloem, required primarily for nutrient transport. Both xylem and phloem are derived from cell divisions in vascular meristems known as the cambium and procambium. One major component that influences several aspects of plant vascular development, including cell division in the vascular meristem, vascular organization and differentiation of vascular cell types, is a signalling module characterized by a peptide ligand called TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) and its cognate receptor, PHLOEM INTERCALATED WITH XYLEM (PXY). In this review, we explore the literature that describes signalling components, phytohormones and transcription factors that interact with these two central factors, to control the varying outputs required in vascular tissues for normal organization and elaboration of plant vascular tissue.
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Affiliation(s)
- J Peter Etchells
- Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Margot E Smit
- Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
| | - Allison Gaudinier
- Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Clara J Williams
- Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
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FUKUDA H. Signaling, transcriptional regulation, and asynchronous pattern formation governing plant xylem development. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:98-107. [PMID: 26972600 PMCID: PMC4925768 DOI: 10.2183/pjab.92.98] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 01/26/2016] [Indexed: 05/07/2023]
Abstract
In plants, vascular stem cells continue to give rise to all xylem and phloem cells, which constitute the plant vascular system. During plant vascular development, the peptide, tracheary element differentiation inhibitory factor (TDIF), regulates vascular stem cell fate in a non-cell-autonomous fashion. TDIF promotes vascular stem cell proliferation through up-regulating the transcription factor gene WUS-related HOMEOBOX4, and it suppresses xylem differentiation from vascular stem cells through the activation of Glycogen Synthase Kinase 3 proteins. VASCULAR-RELATED NAC-DOMAIN6 and 7 (VND6 and 7) are master transcription factors, and ectopic expression of VND6 and VND7 in various plants induces differentiation of different types of cells into metaxylem and protoxylem tracheary elements, respectively. These genes up-regulate genes involved in both patterned secondary cell wall formation and programmed cell death to form tracheary elements. Secondary wall patterns are formed by localized deposition of cellulose microfibrils, which is guided by cortical microtubules. Local activation of the small G-protein, Rho-type 11 determines distribution of cortical microtubules.
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Affiliation(s)
- Hiroo FUKUDA
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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BcMF26a and BcMF26b Are Duplicated Polygalacturonase Genes with Divergent Expression Patterns and Functions in Pollen Development and Pollen Tube Formation in Brassica campestris. PLoS One 2015; 10:e0131173. [PMID: 26153985 PMCID: PMC4495986 DOI: 10.1371/journal.pone.0131173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/31/2015] [Indexed: 12/15/2022] Open
Abstract
Polygalacturonase (PG) is one of the cell wall hydrolytic enzymes involving in pectin degradation. A comparison of two highly conserved duplicated PG genes, namely, Brassica campestris Male Fertility 26a (BcMF26a) and BcMF26b, revealed the different features of their expression patterns and functions. We found that these two genes were orthologous genes of At4g33440, and they originated from a chromosomal segmental duplication. Although structurally similar, their regulatory and intron sequences largely diverged. QRT-PCR analysis showed that the expression level of BcMF26b was higher than that of BcMF26a in almost all the tested organs and tissues in Brassica campestris. Promoter activity analysis showed that, at reproductive development stages, BcMF26b promoter was active in tapetum, pollen grains, and pistils, whereas BcMF26a promoter was only active in pistils. In the subcellular localization experiment, BcMF26a and BcMF26b proteins could be localized to the cell wall. When the two genes were co-inhibited, pollen intine was formed abnormally and pollen tubes could not grow or stretch. Moreover, the knockout mutants of At4g33440 delayed the growth of pollen tubes. Therefore, BcMF26a/b can participate in the construction of pollen wall by modulating intine information and BcMF26b may play a major role in co-inhibiting transformed plants.
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Lyu M, Liang Y, Yu Y, Ma Z, Song L, Yue X, Cao J. Identification and expression analysis of BoMF25, a novel polygalacturonase gene involved in pollen development of Brassica oleracea. PLANT REPRODUCTION 2015; 28:121-132. [PMID: 25967087 DOI: 10.1007/s00497-015-0263-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
BoMF25 acts on pollen wall. Polygalacturonase (PG) is a pectin-digesting enzyme involved in numerous plant developmental processes and is described to be of critical importance for pollen wall development. In the present study, a PG gene, BoMF25, was isolated from Brassica oleracea. BoMF25 is the homologous gene of At4g35670, a PG gene in Arabidopsis thaliana with a high expression level at the tricellular pollen stage. Collinear analysis revealed that the orthologous gene of BoMF25 in Brassica campestris (syn. B. rapa) genome was probably lost because of genome deletion and reshuffling. Sequence analysis indicated that BoMF25 contained four classical conserved domains (I, II, III, and IV) of PG protein. Homology and phylogenetic analyses showed that BoMF25 was clustered in Clade F. The putative promoter sequence, containing classical cis-acting elements and pollen-specific motifs, could drive green fluorescence protein expression in onion epidermal cells. Quantitative RT-PCR analysis suggested that BoMF25 was mainly expressed in the anther at the late stage of pollen development. In situ hybridization analysis also indicated that the strong and specific expression signal of BoMF25 existed in pollen grains at the mature pollen stage. Subcellular localization showed that the fluorescence signal was observed in the cell wall of onion epidermal cells, which suggested that BoMF25 may be a secreted protein localized in the pollen wall.
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Affiliation(s)
- Meiling Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China,
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Dziedzic JA, McDonald AG. In vitro protein profiles in the early and late stages of Douglas-fir xylogenesis. Electrophoresis 2015; 36:2035-45. [PMID: 25999182 DOI: 10.1002/elps.201400561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 04/23/2015] [Accepted: 04/30/2015] [Indexed: 11/09/2022]
Abstract
The process of wood formation is of great interest to control and manipulate wood quality for economically important gymnosperms. A Douglas-fir tissue culture system was developed that could be induced to differentiate into tracheary elements (fibers) making it possible to monitor xylogenesis in vitro by a proteomics approach. Two proteomes were analyzed and compared, one from an early and one from a late stage of the fiber differentiation process. After 18 weeks in a differentiation-inducing medium, 80% of the callus cells were elongated while 20% showed advanced spiral thickening indicating full wood fiber differentiation. Based on 2D electrophoresis, MS, and data analyses (data are available via ProteomeXchange with identifier PXD001484.), it was shown that in nondifferentiated callus (representing an early stage of development), proteins related to protein metabolism, cellular energy, and primary cell wall metabolism were abundant. By comparison, in cells actively differentiating wood fibers (representing a late stage of development), proteins involved in cell wall polysaccharide biosynthesis predominated together with housekeeping and stress-associated proteins.
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Affiliation(s)
| | - Armando G McDonald
- Environmental Science Program, University of Idaho, Moscow, ID, USA.,Renewable Materials Program, Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID, USA
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Nakano Y, Yamaguchi M, Endo H, Rejab NA, Ohtani M. NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. FRONTIERS IN PLANT SCIENCE 2015; 6:288. [PMID: 25999964 PMCID: PMC4419676 DOI: 10.3389/fpls.2015.00288] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/09/2015] [Indexed: 05/08/2023]
Abstract
Plant cells biosynthesize primary cell walls (PCW) in all cells and produce secondary cell walls (SCWs) in specific cell types that conduct water and/or provide mechanical support, such as xylem vessels and fibers. The characteristic mechanical stiffness, chemical recalcitrance, and hydrophobic nature of SCWs result from the organization of SCW-specific biopolymers, i.e., highly ordered cellulose, hemicellulose, and lignin. Synthesis of these SCW-specific biopolymers requires SCW-specific enzymes that are regulated by SCW-specific transcription factors. In this review, we summarize our current knowledge of the transcriptional regulation of SCW formation in plant cells. Advances in research on SCW biosynthesis during the past decade have expanded our understanding of the transcriptional regulation of SCW formation, particularly the functions of the NAC and MYB transcription factors. Focusing on the NAC-MYB-based transcriptional network, we discuss the regulatory systems that evolved in land plants to modify the cell wall to serve as a key component of structures that conduct water and provide mechanical support.
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Affiliation(s)
- Yoshimi Nakano
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Masatoshi Yamaguchi
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan
- PRESTO (Precursory Research for Embryonic Science and Technology), Japan Science and Technology AgencyKawaguchi, Japan
| | - Hitoshi Endo
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Nur Ardiyana Rejab
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
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Sugiyama M. Historical review of research on plant cell dedifferentiation. JOURNAL OF PLANT RESEARCH 2015; 128:349-59. [PMID: 25725626 DOI: 10.1007/s10265-015-0706-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/20/2015] [Indexed: 05/23/2023]
Abstract
Plant cell dedifferentiation has long attracted interest as a key process for understanding the plasticity of plant development. In early studies, typical examples of plant cell dedifferentiation were described as physiological and cytological changes associated with wound healing or regenerative development. Subsequently, plant tissue and cell culture techniques, in which exciting progress was achieved after discovery of the hormonal control of cell proliferation and organogenesis in vitro in the 1950s, have been used extensively to study dedifferentiation. The pioneer studies of plant tissue/cell culture led to the hypothesis that many mature plant cells retain totipotency and related dedifferentiation to the initial step of the expression of totipotency. Plant tissue/cell cultures have provided experimental systems not only for physiological analysis, but also for genetic and molecular biological analysis, of dedifferentiation. More recently, proteomic, transcriptomic, and epigenetic analyses have been applied to the study of plant cell dedifferentiation. All of these works have expanded our knowledge of plant cell dedifferentiation, and current research is contributing to unraveling the molecular mechanisms. The present article provides a brief overview of the history of research on plant cell dedifferentiation.
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Affiliation(s)
- Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, 3-7-1 Hakusan, Bunkyo-ku, Tokyo, 112-0001, Japan,
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Zhong R, Ye ZH. Complexity of the transcriptional network controlling secondary wall biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:193-207. [PMID: 25443846 DOI: 10.1016/j.plantsci.2014.09.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/14/2014] [Accepted: 09/15/2014] [Indexed: 05/02/2023]
Abstract
Secondary walls in the form of wood and fibers are the most abundant biomass produced by vascular plants, and are important raw materials for many industrial uses. Understanding how secondary walls are constructed is of significance in basic plant biology and also has far-reaching implications in genetic engineering of plant biomass better suited for various end uses, such as biofuel production. Secondary walls are composed of three major biopolymers, i.e., cellulose, hemicelluloses and lignin, the biosynthesis of which requires the coordinated transcriptional regulation of all their biosynthesis genes. Genomic and molecular studies have identified a number of transcription factors, whose expression is associated with secondary wall biosynthesis. We comprehensively review how these secondary wall-associated transcription factors function together to turn on the secondary wall biosynthetic program, which leads to secondary wall deposition in vascular plants. The transcriptional network regulating secondary wall biosynthesis employs a multi-leveled feed-forward loop regulatory structure, in which the top-level secondary wall NAC (NAM, ATAF1/2 and CUC2) master switches activate the second-level MYB master switches and they together induce the expression of downstream transcription factors and secondary wall biosynthesis genes. Secondary wall NAC master switches and secondary wall MYB master switches bind to and activate the SNBE (secondary wall NAC binding element) and SMRE (secondary wall MYB-responsive element) sites, respectively, in their target gene promoters. Further investigation of what and how developmental signals trigger the transcriptional network to regulate secondary wall biosynthesis and how different secondary wall-associated transcription factors function cooperatively in activating secondary wall biosynthetic pathways will lead to a better understanding of the molecular mechanisms underlying the transcriptional control of secondary wall biosynthesis.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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Misra BB, Assmann SM, Chen S. Plant single-cell and single-cell-type metabolomics. TRENDS IN PLANT SCIENCE 2014; 19:637-46. [PMID: 24946988 DOI: 10.1016/j.tplants.2014.05.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 05/19/2023]
Abstract
In conjunction with genomics, transcriptomics, and proteomics, plant metabolomics is providing large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense, and productivity. However, dilution effects from organ- and tissue-based sampling of metabolomes have limited our understanding of the intricate regulation of metabolic pathways and networks at the cellular level. Recent advances in metabolomics methodologies, along with the post-genomic expansion of bioinformatics knowledge and functional genomics tools, have allowed the gathering of enriched information on individual cells and single cell types. Here we review progress, current status, opportunities, and challenges presented by single cell-based metabolomics research in plants.
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Affiliation(s)
- Biswapriya B Misra
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sarah M Assmann
- Department of Biology, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
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