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Wang Y, Li Y, Zhang W, Yang Y, Ma Y, Li X, Meng D, Luo H, Xue W, Lv X, Li F, Du W, Geng X. BSA-Seq and Transcriptomic Analysis Provide Candidate Genes Associated with Inflorescence Architecture and Kernel Orientation by Phytohormone Homeostasis in Maize. Int J Mol Sci 2023; 24:10728. [PMID: 37445901 DOI: 10.3390/ijms241310728] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
The developmental plasticity of the maize inflorescence depends on meristems, which directly affect reproductive potential and yield. However, the molecular roles of upper floral meristem (UFM) and lower floral meristem (LFM) in inflorescence and kernel development have not been fully elucidated. In this study, we characterized the reversed kernel1 (rk1) novel mutant, which contains kernels with giant embryos but shows normal vegetative growth like the wild type (WT). Total RNA was extracted from the inflorescence at three stages for transcriptomic analysis. A total of 250.16-Gb clean reads were generated, and 26,248 unigenes were assembled and annotated. Gene ontology analyses of differentially expressed genes (DEGs) detected in the sexual organ formation stage revealed that cell differentiation, organ development, phytohormonal responses and carbohydrate metabolism were enriched. The DEGs associated with the regulation of phytohormone levels and signaling were mainly expressed, including auxin (IAA), jasmonic acid (JA), gibberellins (GA), and abscisic acid (ABA). The transcriptome, hormone evaluation and immunohistochemistry observation revealed that phytohormone homeostasis were affected in rk1. BSA-Seq and transcriptomic analysis also provide candidate genes to regulate UFM and LFM development. These results provide novel insights for understanding the regulatory mechanism of UFM and LFM development in maize and other plants.
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Affiliation(s)
- Yang Wang
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Yang Li
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Wenjie Zhang
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Yue Yang
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuting Ma
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinyang Li
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Dexuan Meng
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Haishan Luo
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Wei Xue
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiangling Lv
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Fenghai Li
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Wanli Du
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaolin Geng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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2
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Ando A, Kirkbride RC, Jones DC, Grimwood J, Chen ZJ. LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation. BMC Genomics 2021; 22:309. [PMID: 33926376 PMCID: PMC8082777 DOI: 10.1186/s12864-021-07579-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/03/2021] [Indexed: 01/21/2023] Open
Abstract
Background Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to understand this dramatic developmental shift have been impeded by the difficulty of separation between fiber and epidermal cells. Results Here we employed laser-capture microdissection (LCM) to separate these cell types. RNA-seq analysis revealed transitional differences between fiber and epidermal-layer cells at 0 or 2 days post anthesis. Specifically, down-regulation of putative cell cycle genes was coupled with upregulation of ribosome biosynthesis and translation-related genes, which may suggest their respective roles in fiber cell initiation. Indeed, the amount of fibers in cultured ovules was increased by cell cycle progression inhibitor, Roscovitine, and decreased by ribosome biosynthesis inhibitor, Rbin-1. Moreover, subfunctionalization of homoeologs was pervasive in fiber and epidermal cells, with expression bias towards 10% more D than A homoeologs of cell cycle related genes and 40–50% more D than A homoeologs of ribosomal protein subunit genes. Key cell cycle regulators were predicted to be epialleles in allotetraploid cotton. MYB-transcription factor genes displayed expression divergence between fibers and ovules. Notably, many phytohormone-related genes were upregulated in ovules and down-regulated in fibers, suggesting spatial-temporal effects on fiber cell development. Conclusions Fiber cell initiation is accompanied by cell cycle arrest coupled with active ribosome biosynthesis, spatial-temporal regulation of phytohormones and MYB transcription factors, and homoeolog expression bias of cell cycle and ribosome biosynthesis genes. These valuable genomic resources and molecular insights will help develop breeding and biotechnological tools to improve cotton fiber production. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07579-1.
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Affiliation(s)
- Atsumi Ando
- Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Don C Jones
- Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
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3
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Chen M, Lin JY, Wu X, Apuya NR, Henry KF, Le BH, Bui AQ, Pelletier JM, Cokus S, Pellegrini M, Harada JJ, Goldberg RB. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proc Natl Acad Sci U S A 2021; 118:e2024704118. [PMID: 33536344 PMCID: PMC8017943 DOI: 10.1073/pnas.2024704118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An important question is what genes govern the differentiation of plant embryos into suspensor and embryo proper regions following fertilization and division of the zygote. We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region. We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones, such as gibberellic acid, and other metabolites are up-regulated in giant scarlet runner bean and common bean suspensors. Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well, strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper. By contrast, genes controlling transcriptional regulation, development, and cell division are up-regulated primarily within the embryo proper. Transcriptomes from less specialized soybean and Arabidopsis suspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated. Genes active in the embryo proper, however, are functionally similar to those active in scarlet runner bean and common bean embryo proper regions. We uncovered a set of suspensor- and embryo proper-specific transcription factors (TFs) that are shared by all embryos irrespective of morphology, suggesting that they are involved in early differentiation processes common to all plants. Chromatin immunoprecipitation sequencing (ChIP-Seq) experiments with scarlet runner bean and soybean WOX9, an up-regulated suspensor TF, gained entry into a regulatory network important for suspensor development irrespective of morphology.
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Affiliation(s)
- Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Xiaomeng Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Nestor R Apuya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Julie M Pelletier
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Shawn Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - John J Harada
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
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Kozieradzka-Kiszkurno M, Majcher D, Brzezicka E, Rojek J, Wróbel-Marek J, Kurczyńska E. Development of Embryo Suspensors for Five Genera of Crassulaceae with Special Emphasis on Plasmodesmata Distribution and Ultrastructure. PLANTS 2020; 9:plants9030320. [PMID: 32138356 PMCID: PMC7154837 DOI: 10.3390/plants9030320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 01/22/2023]
Abstract
The suspensor in the majority of angiosperms is an evolutionally conserved embryonic structure functioning as a conduit that connects ovule tissues with the embryo proper for nutrients and growth factors flux. This is the first study serving the purpose of investigating the correlation between suspensor types and plasmodesmata (PD), by the ultrastructure of this organ in respect of its full development. The special attention is paid to PD in representatives of Crassulaceae genera: Sedum, Aeonium, Monanthes, Aichryson and Echeveria. The contribution of the suspensor in transporting nutrients to the embryo was confirmed by the basal cell structure of the suspensor which produced, on the micropylar side of all genera investigated, a branched haustorium protruding into the surrounding ovular tissue and with wall ingrowths typically associated with cell transfer. The cytoplasm of the basal cell was rich in endoplasmic reticulum, mitochondria, dictyosomes, specialized plastids, microtubules, microbodies and lipid droplets. The basal cell sustained a symplasmic connection with endosperm and neighboring suspensor cells. Our results indicated the dependence of PD ultrastructure on the type of suspensor development: (i) simple PD are assigned to an uniseriate filamentous suspensor and (ii) PD with an electron-dense material are formed in a multiseriate suspensor. The occurrence of only one or both types of PD seems to be specific for the species but not for the genus. Indeed, in the two tested species of Sedum (with the distinct uniseriate/multiseriate suspensors), a diversity in the structure of PD depends on the developmental pattern of the suspensor. In all other genera (with the multiseriate type of development of the suspensor), the one type of electron-dense PD was observed.
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Affiliation(s)
- Małgorzata Kozieradzka-Kiszkurno
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (D.M.); (E.B.); (J.R.)
- Correspondence: ; Tel.: +48-58-5236078
| | - Daria Majcher
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (D.M.); (E.B.); (J.R.)
| | - Emilia Brzezicka
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (D.M.); (E.B.); (J.R.)
| | - Joanna Rojek
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (D.M.); (E.B.); (J.R.)
| | - Justyna Wróbel-Marek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland; (J.W.-M.); (E.K.)
| | - Ewa Kurczyńska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland; (J.W.-M.); (E.K.)
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5
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Chen M, Bui AQ, Goldberg RB. Using Giant Scarlet Runner Bean (Phaseolus coccineus) Embryos to Dissect the Early Events in Plant Embryogenesis. Methods Mol Biol 2020; 2122:205-222. [PMID: 31975305 DOI: 10.1007/978-1-0716-0342-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The giant embryo of the scarlet runner bean (Phaseolus coccineus) has been used historically to investigate the molecular and developmental processes that control the early events of plant embryo development. In more recent years, our laboratory has been using scarlet runner bean embryos to uncover the genes and regulatory events that control embryo proper and suspensor region differentiation shortly after fertilization. In this chapter we describe methods that we have developed to isolate scarlet runner bean embryos at the globular stage of development, and capture embryo proper and suspensor regions by either hand dissection or laser capture microdissection (LCM) for use in downstream genomic analysis. These methods are also applicable for use in investigating the early events of common bean (Phaseolus vulgaris) embryo development, a close relative of scarlet runner bean, which also has a giant embryo in addition to a sequenced genome.
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Affiliation(s)
- Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.,Inviata Ltd., Research Triangle Park, Morrisville, NC, USA
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.
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Kroc M, Koczyk G, Kamel KA, Czepiel K, Fedorowicz-Strońska O, Krajewski P, Kosińska J, Podkowiński J, Wilczura P, Święcicki W. Transcriptome-derived investigation of biosynthesis of quinolizidine alkaloids in narrow-leafed lupin (Lupinus angustifolius L.) highlights candidate genes linked to iucundus locus. Sci Rep 2019; 9:2231. [PMID: 30783128 PMCID: PMC6381137 DOI: 10.1038/s41598-018-37701-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/12/2018] [Indexed: 01/23/2023] Open
Abstract
Unravelling the biosynthetic pathway of quinolizidine alkaloids (QAs), regarded as antinutritional compounds of narrow-leafed lupin (NLL) seeds, is fundamental to best exploit NLL as food or feed. We investigated 12 candidate genes connected to QA biosynthesis, selecting them by transcriptomic and genomic approaches, from the landscape of genes differentially expressed in leaves of the high- and low-alkaloid NLL accessions. Linkage analysis enabled the assessment of the location of the candidate genes in relation to iucundus, a major locus of unknown identity, that confers reduced QA content in seeds. The key finding was the identification of APETALA2/ethylene response transcription factor, RAP2-7, cosegregating with the iucundus locus and located within a region with highly significant QTLs that affect QA composition. We additionally identified a 4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) gene involved in L-lysine biosynthesis as being closely linked to iucundus. The distributed location of other remaining candidates (including previously known QA genes) across different linkage groups, also indirectly supports the transcription factor as a possible regulator of lupin alkaloid biosynthesis. Our findings provide crucial insight into QA biosynthesis in NLL. Additionally, we evaluated and selected appropriate reference genes for qRT-PCRs to analyse the expression levels of QA genes in NLL.
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Affiliation(s)
- Magdalena Kroc
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Grzegorz Koczyk
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Katarzyna A Kamel
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Katarzyna Czepiel
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Olga Fedorowicz-Strońska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Pawińskiego 3c, 02-106, Warsaw, Poland
| | - Jan Podkowiński
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Piotrowo 2, 61-138, Poznań, Poland
| | - Paulina Wilczura
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Wojciech Święcicki
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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7
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Chmielnicka A, Żabka A, Winnicki K, Maszewski J, Polit JT. Endoreplication and its consequences in the suspensor of Pisum sativum. PLANT CELL REPORTS 2018; 37:1639-1651. [PMID: 30132058 PMCID: PMC6244982 DOI: 10.1007/s00299-018-2335-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE DNA replication and continuous process of transcription during ongoing amitotic division accelerate the development of four-celled pea suspensor containing nuclei which create transient gradient of polyploidy necessary for correct embryo development. A suspensor, the link between embryo proper and surrounding tissues, differs significantly in size, morphology, and degree of polyploidy among the species. The suspensor of Pisum sativum consists of four polynuclear cells (two hemispherical and two elongated) formed in two layers. Their nuclei undergo endoreplication reaching, respectively, up to 256C and 128-256C DNA levels in its hemispherical and elongated parts. Our study shows that endoreplication first appears in the spherical part of the suspensor, and, subsequently, in the elongated one. At the next stages of suspensor development, the increase in DNA content takes place also in a similar order. Thus, despite simple construction of the suspensor, its development, supported by endoreplication, creates a certain gradient of polyploidy, which occurs in more extensive suspensors. Moreover, the rapid development of suspensor is supported both by the initiation of DNA replication prior to the completion of amitotic division of its polyploidal nuclei and by a continuous process of transcription, which is silenced by chromatin condensation throughout mitosis. Furthermore, the increase in DNA content correlates with the greater amount of transcripts; however, the multiplication of DNA copies does not entail an increase (but fluctuation) in the mean transcriptional activity of a particular nucleus during the next stages of suspensor development.
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Affiliation(s)
- Agnieszka Chmielnicka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland
| | - Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland
| | - Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
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8
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Bureau C, Lanau N, Ingouff M, Hassan B, Meunier AC, Divol F, Sevilla R, Mieulet D, Dievart A, Périn C. A protocol combining multiphoton microscopy and propidium iodide for deep 3D root meristem imaging in rice: application for the screening and identification of tissue-specific enhancer trap lines. PLANT METHODS 2018; 14:96. [PMID: 30386414 PMCID: PMC6206838 DOI: 10.1186/s13007-018-0364-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The clear visualization of 3D organization at the cellular level in plant tissues is needed to fully understand plant development processes. Imaging tools allow the visualization of the main fluorophores and in vivo growth monitoring. Confocal microscopy coupled with the use of propidium iodide (PI) counter-staining is one of the most popular tools used to characterize the structure of root meristems in A. thaliana. However, such an approach is relatively ineffective in species with more complex and thicker root systems. RESULTS We adapted a PI counter-staining protocol to visualize the internal 3D architecture of rice root meristems using multiphoton microscopy. This protocol is simple and compatible with the main fluorophores (CFP, GFP and mCherry). The efficiency and applicability of this protocol were demonstrated by screening a population of 57 enhancer trap lines. We successfully characterized GFP expression in all of the lines and identified 5 lines with tissue-specific expression. CONCLUSIONS All of these resources are now available for the rice community and represent critical tools for future studies of root development.
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Affiliation(s)
- Charlotte Bureau
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Nadège Lanau
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Mathieu Ingouff
- UMR DIADE, Université de Montpellier, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France
| | - Boukhaddaoui Hassan
- INSERM U1051, Institut des Neurosciences de Montpellier, 34095 Montpellier, France
| | - Anne-Cécile Meunier
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Fanchon Divol
- UMR Biochimie et Physiologie Moléculaire des Plantes, INRA, Campus INRA/SupAgro, 2 Place Viala, 34060 Montpellier Cedex 2, France
| | - Rosie Sevilla
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Delphine Mieulet
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Anne Dievart
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Christophe Périn
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
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9
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Henry KF, Bui AQ, Kawashima T, Goldberg RB. A shared cis-regulatory module activates transcription in the suspensor of plant embryos. Proc Natl Acad Sci U S A 2018; 115:E5824-E5833. [PMID: 29866850 PMCID: PMC6016821 DOI: 10.1073/pnas.1805802115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mechanisms controlling the transcription of gene sets in specific regions of a plant embryo shortly after fertilization remain unknown. Previously, we showed that G564 mRNA, encoding a protein of unknown function, accumulates to high levels in the giant suspensor of both Scarlet Runner Bean (SRB) and Common Bean embryos, and a cis-regulatory module containing three unique DNA sequences, designated as the 10-bp, Region 2, and Fifth motifs, is required for G564 suspensor-specific transcription [Henry KF, et al. (2015) Plant Mol Biol 88:207-217; Kawashima T, et al. (2009) Proc Natl Acad Sci USA 106:3627-3632]. We tested the hypothesis that these motifs are also required for transcription of the SRB GA 20-oxidase gene, which encodes a gibberellic acid hormone biosynthesis enzyme and is coexpressed with G564 at a high level in giant bean suspensors. We used deletion and gain-of-function experiments in transgenic tobacco embryos to show that two GA 20-oxidase DNA regions are required for suspensor-specific transcription, one in the 5' UTR (+119 to +205) and another in the 5' upstream region (-341 to -316). Mutagenesis of sequences in these two regions determined that the cis-regulatory motifs required for G564 suspensor transcription are also required for GA 20-oxidase transcription within the suspensor, although the motif arrangement differs. Our results demonstrate the flexibility of motif positioning within a cis-regulatory module that activates gene transcription within giant bean suspensors and suggest that G564 and GA 20-oxidase comprise part of a suspensor gene regulatory network.
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Affiliation(s)
- Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Tomokazu Kawashima
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
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10
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Simon C, Lion C, Huss B, Blervacq AS, Spriet C, Guérardel Y, Biot C, Hawkins S. BLISS: Shining a light on lignification in plants. PLANT SIGNALING & BEHAVIOR 2017; 12:e1359366. [PMID: 28786751 PMCID: PMC5616161 DOI: 10.1080/15592324.2017.1359366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
Lignin is a polyphenolic polymer of the plant cell wall formed by the oxidative polymerization of 3 main monomers called monolignols that give rise to the lignin H-, G- and S-units. Together with cellulose and hemicelluloses, lignin is a major component of plant biomass that is widely exploited by humans in numerous industrial processes. Despite recent advances in our understanding of monolignol biosynthesis, our current understanding of the spatio-temporal regulation of their transport and polymerization is more limited. In a recent publication, we have reported the development of an original Bioorthogonal Labeling Imaging Sequential Strategy (BLISS) that allows us to visualize the simultaneous incorporation dynamics of H and G monolignol reporters into lignifying cell walls of the flax stem. 11 Here, we extend the application of this strategy to other plant organs such as roots and rapidly discuss some of the contributions and perspectives of this new technique for improving our understanding of the lignification process in plants.
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Affiliation(s)
- Clémence Simon
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Cedric Lion
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Brigitte Huss
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Anne-Sophie Blervacq
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Corentin Spriet
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Yann Guérardel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Christophe Biot
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille,France
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11
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Igielski R, Kępczyńska E. Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn. PLoS One 2017; 12:e0182055. [PMID: 28750086 PMCID: PMC5531487 DOI: 10.1371/journal.pone.0182055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/11/2017] [Indexed: 01/02/2023] Open
Abstract
Gibberellins (GAs) are involved in the regulation of numerous developmental processes in plants including zygotic embryogenesis, but their biosynthesis and role during somatic embryogenesis (SE) is mostly unknown. In this study we show that during three week- long induction phase, when cells of leaf explants from non-embryogenic genotype (M9) and embryogenic variant (M9-10a) were forming the callus, all the bioactive gibberellins from non-13-hydroxylation (GA4, GA7) and 13-hydroxylation (GA1, GA5, GA3, GA6) pathways were present, but the contents of only a few of them differed between the tested lines. The GA53 and GA19 substrates synthesized by the 13-hydroxylation pathway accumulated specifically in the M9-10a line after the first week of induction; subsequently, among the bioactive gibberellins detected, only the content of GA3 increased and appeared to be connected with acquisition of embryogenic competence. We fully annotated 20 Medicago truncatula orthologous genes coding the enzymes which catalyze all the known reactions of gibberellin biosynthesis. Our results indicate that, within all the genes tested, expression of only three: MtCPS, MtGA3ox1 and MtGA3ox2, was specific to embryogenic explants and reflected the changes observed in GA53, GA19 and GA3 contents. Moreover, by analyzing expression of MtBBM, SE marker gene, we confirmed the inhibitory effect of manipulation in GAs metabolism, applying exogenous GA3, which not only impaired the production of somatic embryos, but also significantly decreased expression of this gene.
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Affiliation(s)
- Rafał Igielski
- Department of Plant Biotechnology, University of Szczecin, Szczecin, Poland
| | - Ewa Kępczyńska
- Department of Plant Biotechnology, University of Szczecin, Szczecin, Poland
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12
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Igielski R, Kępczyńska E. Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn. PLoS One 2017; 12:e0182055. [PMID: 28750086 DOI: 10.1371/journal.pone.018205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/11/2017] [Indexed: 05/18/2023] Open
Abstract
Gibberellins (GAs) are involved in the regulation of numerous developmental processes in plants including zygotic embryogenesis, but their biosynthesis and role during somatic embryogenesis (SE) is mostly unknown. In this study we show that during three week- long induction phase, when cells of leaf explants from non-embryogenic genotype (M9) and embryogenic variant (M9-10a) were forming the callus, all the bioactive gibberellins from non-13-hydroxylation (GA4, GA7) and 13-hydroxylation (GA1, GA5, GA3, GA6) pathways were present, but the contents of only a few of them differed between the tested lines. The GA53 and GA19 substrates synthesized by the 13-hydroxylation pathway accumulated specifically in the M9-10a line after the first week of induction; subsequently, among the bioactive gibberellins detected, only the content of GA3 increased and appeared to be connected with acquisition of embryogenic competence. We fully annotated 20 Medicago truncatula orthologous genes coding the enzymes which catalyze all the known reactions of gibberellin biosynthesis. Our results indicate that, within all the genes tested, expression of only three: MtCPS, MtGA3ox1 and MtGA3ox2, was specific to embryogenic explants and reflected the changes observed in GA53, GA19 and GA3 contents. Moreover, by analyzing expression of MtBBM, SE marker gene, we confirmed the inhibitory effect of manipulation in GAs metabolism, applying exogenous GA3, which not only impaired the production of somatic embryos, but also significantly decreased expression of this gene.
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Affiliation(s)
- Rafał Igielski
- Department of Plant Biotechnology, University of Szczecin, Szczecin, Poland
| | - Ewa Kępczyńska
- Department of Plant Biotechnology, University of Szczecin, Szczecin, Poland
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Henry KF, Kawashima T, Goldberg RB. A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements. PLANT MOLECULAR BIOLOGY 2015; 88:207-17. [PMID: 25796517 PMCID: PMC4441743 DOI: 10.1007/s11103-015-0308-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/13/2015] [Indexed: 05/08/2023]
Abstract
Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we use site-directed mutagenesis experiments in transgenic tobacco globular-stage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. A homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.
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Affiliation(s)
- Kelli F. Henry
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Dr. East, Los Angeles, CA 90095-7239 USA
| | - Tomokazu Kawashima
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Dr. East, Los Angeles, CA 90095-7239 USA
- Present Address: Gregor Mendel Institute, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Robert B. Goldberg
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Dr. East, Los Angeles, CA 90095-7239 USA
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