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Wang W, Zheng H. Arabidopsis reticulons inhibit ROOT HAIR DEFECTIVE3 to form a stable tubular endoplasmic reticulum network. PLANT PHYSIOLOGY 2024; 194:1431-1446. [PMID: 37879114 DOI: 10.1093/plphys/kiad574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
The endoplasmic reticulum (ER) is a network of interconnected tubules and sheets stretching throughout the cytoplasm of plant cells. In Arabidopsis (Arabidopsis thaliana), ROOT HAIR DEFECTIVE3 (RHD3) mediates ER tubule fusion, while reticulon proteins induce ER membrane curvature to produce ER tubules. However, it is unclear if and how RHD3-reticulon interplay during the formation of the interconnected tubular ER network. We discovered that RHD3 physically interacts with Arabidopsis reticulon proteins, including reticulon-like protein subfamily B3 (RTNLB3), on ER tubules and at 3-way junctions of the ER. The RTNLB3 protein is widely expressed in Arabidopsis seedlings and localizes to ER tubules. Although the growth of knockout rtnlb3 mutant plants was relatively normal, root hairs of rtnlb3 were shorter than those of wild type. The ER in mature mutant cells was also more sheeted than that in wild type. rhd3 is known to have short roots and root hairs and less branched ER tubules in cells. Interestingly, rtnlb3 genetically antagonizes rhd3 in plant root development and in ER interconnectivity. We show that reticulons including RTNLB3 inhibit the ER fusion activity of RHD3, partly by interfering with RHD3 dimerization. We conclude that reticulon proteins negatively regulate RHD3 to balance its ER fusion activity for the formation of a stable tubular ER network in plant cell growth.
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Affiliation(s)
- Weina Wang
- Department of Biology, McGill University, 1205 Dr. Penfield Avenue, Montreal, QC H3A 1B1, Canada
| | - Huanquan Zheng
- Department of Biology, McGill University, 1205 Dr. Penfield Avenue, Montreal, QC H3A 1B1, Canada
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2
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Bogomolov A, Zolotareva K, Filonov S, Chadaeva I, Rasskazov D, Sharypova E, Podkolodnyy N, Ponomarenko P, Savinkova L, Tverdokhleb N, Khandaev B, Kondratyuk E, Podkolodnaya O, Zemlyanskaya E, Kolchanov NA, Ponomarenko M. AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L. Int J Mol Sci 2024; 25:607. [PMID: 38203780 PMCID: PMC10779315 DOI: 10.3390/ijms25010607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/18/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.
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Affiliation(s)
- Anton Bogomolov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Sergey Filonov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Natalya Tverdokhleb
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Bato Khandaev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk 630501, Novosibirsk Region, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
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Pan J, Li W, Chen B, Liu L, Zhang J, Li J. Arabidopsis 3β-Hydroxysteroid Dehydrogenases/C4-Decarboxylases Are Essential for the Pollen and Embryonic Development. Int J Mol Sci 2023; 24:15565. [PMID: 37958553 PMCID: PMC10649741 DOI: 10.3390/ijms242115565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The biosynthesis of C27-29 sterols from their C30 precursor squalene involves C24-alkylation and the removal of three methyl groups, including two at the C4 position. The two C4 demethylation reactions require a bifunctional enzyme known as 3β-hydroxysteroid dehydrogenase/C4-decarboxylase (3βHSD/D), which removes an oxidized methyl (carboxylic) group at C4 while simultaneously catalyzing the 3β-hydroxyl→3-keto oxidation. Its loss-of-function mutations cause ergosterol-dependent growth in yeast and congenital hemidysplasia with ichthyosiform erythroderma and limb defect (CHILD) syndrome in humans. Although plant 3βHSD/D enzymes were well studied enzymatically, their developmental functions remain unknown. Here we employed a CRISPR/Cas9-based genome-editing approach to generate knockout mutants for two Arabidopsis 3βHSD/D genes, HSD1 and HSD2, and discovered the male gametophytic lethality for the hsd1 hsd2 double mutation. Pollen-specific expression of HSD2 in the heterozygous hsd1 hsd2/+ mutant not only rescued the pollen lethality but also revealed the critical roles of the two HSD genes in embryogenesis. Our study thus demonstrated the essential functions of the two Arabidopsis 3βHSD/D genes in male gametogenesis and embryogenesis.
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Affiliation(s)
- Jiawen Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (J.P.); (W.L.); (B.C.); (L.L.)
| | - Weifeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (J.P.); (W.L.); (B.C.); (L.L.)
| | - Binzhao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (J.P.); (W.L.); (B.C.); (L.L.)
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (J.P.); (W.L.); (B.C.); (L.L.)
| | - Jianjun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (J.P.); (W.L.); (B.C.); (L.L.)
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (J.P.); (W.L.); (B.C.); (L.L.)
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
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4
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Wang P, Duckney P, Gao E, Hussey PJ, Kriechbaumer V, Li C, Zang J, Zhang T. Keep in contact: multiple roles of endoplasmic reticulum-membrane contact sites and the organelle interaction network in plants. THE NEW PHYTOLOGIST 2023; 238:482-499. [PMID: 36651025 DOI: 10.1111/nph.18745] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Functional regulation and structural maintenance of the different organelles in plants contribute directly to plant development, reproduction and stress responses. To ensure these activities take place effectively, cells have evolved an interconnected network amongst various subcellular compartments, regulating rapid signal transduction and the exchange of biomaterial. Many proteins that regulate membrane connections have recently been identified in plants, and this is the first step in elucidating both the mechanism and function of these connections. Amongst all organelles, the endoplasmic reticulum is the key structure, which likely links most of the different subcellular compartments through membrane contact sites (MCS) and the ER-PM contact sites (EPCS) have been the most intensely studied in plants. However, the molecular composition and function of plant MCS are being found to be different from other eukaryotic systems. In this article, we will summarise the most recent advances in this field and discuss the mechanism and biological relevance of these essential links in plants.
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Affiliation(s)
- Pengwei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Patrick Duckney
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Erlin Gao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Patrick J Hussey
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Chengyang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jingze Zang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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5
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Pereira Neto LG, Rossini BC, Marino CL, Toorop PE, Silva EAA. Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil. Int J Mol Sci 2022; 23:ijms232213852. [PMID: 36430327 PMCID: PMC9696909 DOI: 10.3390/ijms232213852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Astronium fraxinifolium Schott (Anacardiaceae), also known as a 'gonçalo-alves', is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium.
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Affiliation(s)
| | - Bruno Cesar Rossini
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Correspondence:
| | - Celso Luis Marino
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Departament of Biological and Chemical Sciences, Biosciences Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18618-689, Brazil
| | - Peter E. Toorop
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Edvaldo Aparecido Amaral Silva
- Departamento de Produção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu 18610-034, Brazil
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Kontou A, Herman EK, Field MC, Dacks JB, Koumandou VL. Evolution of factors shaping the endoplasmic reticulum. Traffic 2022; 23:462-473. [PMID: 36040076 PMCID: PMC9804665 DOI: 10.1111/tra.12863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 01/09/2023]
Abstract
Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.
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Affiliation(s)
- Aspasia Kontou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
| | - Emily K. Herman
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Present address:
Department of Agricultural, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeDundeeUK,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and EnvironmentUniversity College of LondonLondonUK
| | - V. Lila Koumandou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
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Ishikawa K, Konno R, Hirano S, Fujii Y, Fujiwara M, Fukao Y, Kodama Y. The endoplasmic reticulum membrane-bending protein RETICULON facilitates chloroplast relocation movement in Marchantia polymorpha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:205-216. [PMID: 35476214 DOI: 10.1111/tpj.15787] [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: 02/21/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Plant cells alter the intracellular positions of chloroplasts to ensure efficient photosynthesis, a process controlled by the blue light receptor phototropin. Chloroplasts migrate toward weak light (accumulation response) and move away from excess light (avoidance response). Chloroplasts are encircled by the endoplasmic reticulum (ER), which forms a complex network throughout the cytoplasm. To ensure rapid chloroplast relocation, the ER must alter its structure in conjunction with chloroplast relocation movement, but little is known about the underlying mechanism. Here, we searched for interactors of phototropin in the liverwort Marchantia polymorpha and identified a RETICULON (RTN) family protein; RTN proteins play central roles in ER tubule formation and ER network maintenance by stabilizing the curvature of ER membranes in eukaryotic cells. Marchantia polymorpha RTN1 (MpRTN1) is localized to ER tubules and the rims of ER sheets, which is consistent with the localization of RTNs in other plants and heterotrophs. The Mprtn1 mutant showed an increased ER tubule diameter, pointing to a role for MpRTN1 in ER membrane constriction. Furthermore, Mprtn1 showed a delayed chloroplast avoidance response but a normal chloroplast accumulation response. The live cell imaging of ER dynamics revealed that ER restructuring was impaired in Mprtn1 during the chloroplast avoidance response. These results suggest that during the chloroplast avoidance response, MpRTN1 restructures the ER network and facilitates chloroplast movement via an interaction with phototropin. Our findings provide evidence that plant cells respond to fluctuating environmental conditions by controlling the movements of multiple organelles in a synchronized manner.
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Affiliation(s)
- Kazuya Ishikawa
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Ryota Konno
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Satoyuki Hirano
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Yuta Fujii
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Masayuki Fujiwara
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
- YANMAR HOLDINGS Co. Ltd., Osaka, Japan
| | - Yoichiro Fukao
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
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8
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Kriechbaumer V, Botchway SW. Methods for Detection of Protein Interactions with Plasmodesmata-Localized Reticulons. Methods Mol Biol 2022; 2457:209-218. [PMID: 35349142 DOI: 10.1007/978-1-0716-2132-5_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: 06/14/2023]
Abstract
Plant reticulon family proteins (RTN) tubulate the ER by dimerization and oligomerization, creating localized ER membrane tensions that result in membrane curvature. Two RTN ER-shaping proteins have been found in the plasmodesmata (PD) proteome which could potentially contribute to the formation of the desmotubule, an ER-derived structure that crosses primary PD and physically connects the ER of two cells. Here we describe two methods used to identify partners of two PD-resident reticulon proteins, RTN3 and RTN6 that are located in primary PD at cytokinesis in tobacco (Nicotiana tabacum): immunoprecipitations using GFP-Trap®_A beads to find novel interaction partners and FRET-FLIM to test for and quantify direct protein-protein interactions in planta.
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Affiliation(s)
- Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC), Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
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In Planta Labeling Using a Clickable ER-Disrupting Probe Suggests a Role for Oleosins in Arabidopsis Seedling ER Integrity. ACS Chem Biol 2021; 16:2151-2157. [PMID: 34505514 DOI: 10.1021/acschembio.1c00607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several small-molecule perturbagens of the plant endomembrane system are known, but few selectively disrupt endoplasmic reticulum (ER) structure and function. We conducted a microscopy-based screen for small-molecule disruptors of ER structure and discovered eroonazole, a 1,2-4-triazole that induces extensive ER vesiculation in Arabidopsis seedlings. To identify eroonazole targets, we synthesized a clickable photoaffinity derivative and used it for whole-seedling labeling experiments. These reveal that the probe labels multiple oleosins, plant membrane proteins that stabilize ER-derived lipid droplets. Oleosin labeling is absent in an oleosin1234 quadruple mutant and reduced using an inactive analog. Cellular analyses of the ER in the quadruple mutant demonstrate that oleosins are required for normal ER structure during seed germination and suggest that perturbation of oleosin function by eroonazole underlies its effects on seedling ER structure.
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10
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Kumar K, Gibbs HC, Yeh AT, Griffing LR. The Sterol Trafficking Pathway in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:616631. [PMID: 34122463 PMCID: PMC8187924 DOI: 10.3389/fpls.2021.616631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
In plants, the trafficking mechanisms by which sterols move through the plant and into target cells are unknown. Earlier studies identified endosomes as primary candidates for internalization of sterols in plants, but these results have come into question. Here, we show that in elongating root cells, the internalization of sterol occurs primarily by a non-endocytic mechanism. Added fluorescent sterols [dehydroergosterol (DHE) and BODIPY-cholesterol (BCh)] do not initially label endosomes identified by fluorescent protein markers or by internalized FM4-64. Instead, the nuclear envelope, an organelle not associated with the endocytic pathway but part of the endoplasmic reticulum (ER), becomes labeled. This result is supported by experiments with the inducible overexpression of auxilin-2-like protein (AUX2 line), which blocks most endocytosis upon induction. Internalization and nuclear envelope labeling still occur in induced AUX2 cells. Longer-term incubation labels the oil body, a site involved in sterol storage. Although the first site of localization, the nuclear envelope, is part of the ER, other domains of the ER do not accumulate the label. The trafficking pathway differs from vesicular endocytosis and points toward a different pathway of sterol transport possibly involving other mechanisms, such as ER-plasma membrane contact sites and cytoplasmic transport.
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Affiliation(s)
- Krishna Kumar
- Molecular and Environmental Plant Sciences Interdisciplinary Program, Texas A&M University, College Station, TX, United States
| | - Holly C. Gibbs
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
- Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
| | - Alvin T. Yeh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Lawrence R. Griffing
- Molecular and Environmental Plant Sciences Interdisciplinary Program, Texas A&M University, College Station, TX, United States
- Department of Biology, Texas A&M University, College Station, TX, United States
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11
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Brooks RL, Mistry CS, Dixon AM. Curvature sensing amphipathic helix in the C-terminus of RTNLB13 is conserved in all endoplasmic reticulum shaping reticulons in Arabidopsis thaliana. Sci Rep 2021; 11:6326. [PMID: 33737685 PMCID: PMC7973432 DOI: 10.1038/s41598-021-85866-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 11/24/2022] Open
Abstract
The reticulon family of integral membrane proteins are conserved across all eukaryotes and typically localize to the endoplasmic reticulum (ER), where they are involved in generating highly-curved tubules. We recently demonstrated that Reticulon-like protein B13 (RTNLB13) from Arabidopsis thaliana contains a curvature-responsive amphipathic helix (APH) important for the proteins' ability to induce curvature in the ER membrane, but incapable of generating curvature by itself. We suggested it acts as a feedback element, only folding/binding once a sufficient degree of curvature has been achieved, and stabilizes curvature without disrupting the bilayer. However, it remains unclear whether this is unique to RTNLB13 or is conserved across all reticulons-to date, experimental evidence has only been reported for two reticulons. Here we used biophysical methods to characterize a minimal library of putative APH peptides from across the 21 A. thaliana isoforms. We found that reticulons with the closest evolutionary relationship to RTNLB13 contain curvature-sensing APHs in the same location with sequence conservation. Our data reveal that a more distantly-related branch of reticulons developed a ~ 20-residue linker between the transmembrane domain and APH. This may facilitate functional flexibility as previous studies have linked these isoforms not only to ER remodeling but other cellular activities.
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Affiliation(s)
- Rhiannon L Brooks
- MAS Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Chandni S Mistry
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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12
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Kriechbaumer V, Brandizzi F. The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions. J Microsc 2020; 280:122-133. [PMID: 32426862 PMCID: PMC10895883 DOI: 10.1111/jmi.12909] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.
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Affiliation(s)
- V Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, U.K
| | - F Brandizzi
- MSU-DOE Plant Research Laboratory, Department of Plant Biology, Michigan State University, East Lansing, Michigan, U.S.A
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13
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McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux SJ, Browning KS, Chen ZJ, Ronald PC, Marcotte EM. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. Cell 2020; 181:460-474.e14. [PMID: 32191846 DOI: 10.1016/j.cell.2020.02.049] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/08/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023]
Abstract
Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.
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Affiliation(s)
- Claire D McWhite
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Kevin Drew
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Rachael M Cox
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Viviana June
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Cuihong Wan
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA; Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, P.R. China
| | - Mari L Salmi
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Karen S Browning
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Pamela C Ronald
- Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
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14
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Zhang X, Ding X, Marshall RS, Paez-Valencia J, Lacey P, Vierstra RD, Otegui MS. Reticulon proteins modulate autophagy of the endoplasmic reticulum in maize endosperm. eLife 2020; 9:51918. [PMID: 32011236 PMCID: PMC7046470 DOI: 10.7554/elife.51918] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/02/2020] [Indexed: 12/18/2022] Open
Abstract
Reticulon (Rtn) proteins shape tubular domains of the endoplasmic reticulum (ER), and in some cases are autophagy receptors for selective ER turnover. We have found that maize Rtn1 and Rtn2 control ER homeostasis and autophagic flux in endosperm aleurone cells, where the ER accumulates lipid droplets and synthesizes storage protein accretions metabolized during germination. Maize Rtn1 and Rtn2 are expressed in the endosperm, localize to the ER, and re-model ER architecture in a dose-dependent manner. Rtn1 and Rtn2 interact with Atg8a using four Atg8-interacting motifs (AIMs) located at the C-terminus, cytoplasmic loop, and within the transmembrane segments. Binding between Rtn2 and Atg8 is elevated upon ER stress. Maize rtn2 mutants display increased autophagy and up-regulation of an ER stress-responsive chaperone. We propose that maize Rtn1 and Rtn2 act as receptors for autophagy-mediated ER turnover, and thus are critical for ER homeostasis and suppression of ER stress.
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Affiliation(s)
- Xiaoguo Zhang
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | - Xinxin Ding
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | | | - Julio Paez-Valencia
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | - Patrick Lacey
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | | | - Marisa S Otegui
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States.,Department of Genetics, University of Wisconsin, Madison, United States
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15
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Plasmodesmata Conductivity Regulation: A Mechanistic Model. PLANTS 2019; 8:plants8120595. [PMID: 31842374 PMCID: PMC6963776 DOI: 10.3390/plants8120595] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/03/2019] [Accepted: 12/10/2019] [Indexed: 01/16/2023]
Abstract
Plant cells form a multicellular symplast via cytoplasmic bridges called plasmodesmata (Pd) and the endoplasmic reticulum (ER) that crosses almost all plant tissues. The Pd proteome is mainly represented by secreted Pd-associated proteins (PdAPs), the repertoire of which quickly adapts to environmental conditions and responds to biotic and abiotic stresses. Although the important role of Pd in stress-induced reactions is universally recognized, the mechanisms of Pd control are still not fully understood. The negative role of callose in Pd permeability has been convincingly confirmed experimentally, yet the roles of cytoskeletal elements and many PdAPs remain unclear. Here, we discuss the contribution of each protein component to Pd control. Based on known data, we offer mechanistic models of mature leaf Pd regulation in response to stressful effects.
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16
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Affiliation(s)
- ULLA NEUMANN
- Max Planck Institute for Plant Breeding ResearchCentral Microscopy Cologne Germany
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17
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Platre MP, Noack LC, Doumane M, Bayle V, Simon MLA, Maneta-Peyret L, Fouillen L, Stanislas T, Armengot L, Pejchar P, Caillaud MC, Potocký M, Čopič A, Moreau P, Jaillais Y. A Combinatorial Lipid Code Shapes the Electrostatic Landscape of Plant Endomembranes. Dev Cell 2018; 45:465-480.e11. [PMID: 29754803 DOI: 10.1016/j.devcel.2018.04.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 03/06/2018] [Accepted: 04/11/2018] [Indexed: 12/21/2022]
Abstract
Membrane surface charge is critical for the transient, yet specific recruitment of proteins with polybasic regions to certain organelles. In eukaryotes, the plasma membrane (PM) is the most electronegative compartment of the cell, which specifies its identity. As such, membrane electrostatics is a central parameter in signaling, intracellular trafficking, and polarity. Here, we explore which are the lipids that control membrane electrostatics using plants as a model. We show that phosphatidylinositol-4-phosphate (PI4P), phosphatidic acidic (PA), and phosphatidylserine (PS) are separately required to generate the electrostatic signature of the plant PM. In addition, we reveal the existence of an electrostatic territory that is organized as a gradient along the endocytic pathway and is controlled by PS/PI4P combination. Altogether, we propose that combinatorial lipid composition of the cytosolic leaflet of organelles not only defines the electrostatic territory but also distinguishes different functional compartments within this territory by specifying their varying surface charges.
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Affiliation(s)
- Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Mehdi Doumane
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Mathilde Laetitia Audrey Simon
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Lilly Maneta-Peyret
- UMR 5200 Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, Bâtiment A3 - INRA Bordeaux Aquitaine, 71 Avenue Edouard Bourlaux- CS 20032, Villenave d'Ornon 33140, France
| | - Laetitia Fouillen
- UMR 5200 Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, Bâtiment A3 - INRA Bordeaux Aquitaine, 71 Avenue Edouard Bourlaux- CS 20032, Villenave d'Ornon 33140, France; Metabolome-Lipidome Facility of Bordeaux, Functional Genomics Center, Villenave d'Ornon, France
| | - Thomas Stanislas
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Přemysl Pejchar
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6 - Lysolaje, Czech Republic
| | - Marie-Cécile Caillaud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France
| | - Martin Potocký
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6 - Lysolaje, Czech Republic
| | - Alenka Čopič
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris 75013, France
| | - Patrick Moreau
- UMR 5200 Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, Bâtiment A3 - INRA Bordeaux Aquitaine, 71 Avenue Edouard Bourlaux- CS 20032, Villenave d'Ornon 33140, France; Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, University of Bordeaux, Bordeaux 33000, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon 69342, France.
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