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Wallner ES, Dolan L. Reproducibly oriented cell divisions pattern the prothallus to set up dorsoventrality and de novo meristem formation in Marchantia polymorpha. Curr Biol 2024:S0960-9822(24)01070-4. [PMID: 39191253 DOI: 10.1016/j.cub.2024.07.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 08/29/2024]
Abstract
Land plant bodies develop from stem cells located in meristems. However, we know little about how meristems initiate from non-meristematic cells. The haploid body of bryophytes develops from unicellular spores in isolation from the parental plant, which allows all stages of development to be observed. We discovered that the Marchantia spore undergoes a series of reproducibly oriented cell divisions to generate a flat prothallus on which a meristem later develops de novo. The young sporeling comprises an early cell mass. One cell of the early cell mass elongates and undergoes a formative division that produces the prothalloblast, which initiates prothallus formation. A symmetric division of the prothalloblast followed by two transverse divisions generates a four-celled plate that expands into a flat disc through oblique divisions in three of the four plate-cell-derived quadrants. One quadrant gives rise to a flat flabellum. A notch with a meristem and apical stem cell develops at the margin of the flabellum. The transcription factor Marchantia class III homeodomain-leucine-zipper (MpC3HDZ) is a marker of the first flat prothallus structure and polarizes to the dorsal tissues of flabella and meristems. Mpc3hdz mutants are defective in setting up dorsoventrality and thallus body flatness. We report how a regular set of cell divisions forms the prothallus-the first dorsoventral structure-and how cells on the margin of the prothallus develop a dorsoventralized meristem de novo.
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Affiliation(s)
| | - Liam Dolan
- Gregor Mendel Institute, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria.
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2
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Romani F, Sauret-Güeto S, Rebmann M, Annese D, Bonter I, Tomaselli M, Dierschke T, Delmans M, Frangedakis E, Silvestri L, Rever J, Bowman JL, Romani I, Haseloff J. The landscape of transcription factor promoter activity during vegetative development in Marchantia. THE PLANT CELL 2024; 36:2140-2159. [PMID: 38391349 PMCID: PMC11132968 DOI: 10.1093/plcell/koae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/08/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024]
Abstract
Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.
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Affiliation(s)
- Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Davide Annese
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Ignacy Bonter
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Linda Silvestri
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Ignacio Romani
- Departamento de Ciencias Sociales, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
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3
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Mohanasundaram B, Palit S, Bhide AJ, Pala M, Rajoria K, Girigosavi P, Banerjee AK. PpSCARECROW1 (PpSCR1) regulates leaf blade and mid-vein development in Physcomitrium patens. PLANT MOLECULAR BIOLOGY 2024; 114:12. [PMID: 38324222 DOI: 10.1007/s11103-023-01398-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 12/11/2023] [Indexed: 02/08/2024]
Abstract
In plants, asymmetric cell divisions result in distinct cell fates forming large and small daughter cells, adding to the cellular diversity in an organ. SCARECROW (SCR), a GRAS domain-containing transcription factor controls asymmetric periclinal cell divisions in flowering plants by governing radial patterning of ground tissue in roots and cell proliferation in leaves. Though SCR homologs are present across land plant lineages, the current understanding of their role in cellular patterning and leaf development is mostly limited to flowering plants. Our phylogenetic analysis identified three SCR homologs in moss Physcomitrium patens, amongst which PpSCR1 showed highest expression in gametophores and its promoter activity was prominent at the mid-vein and the flanking leaf blade cells pointing towards its role in leaf development. Notably, out of the three SCR homologs, only the ppscr1 knock-out lines developed slender leaves with four times narrower leaf blade and three times thicker mid-vein. Detailed histology studies revealed that slender leaf phenotype is either due to the loss of anticlinal cell divisions or failure of periclinal division suppression in the leaf blade. RNA-Seq analyses revealed that genes responsible for cell division and differentiation are expressed differentially in the mutant. PpSCR1 overexpression lines exhibited significantly wider leaf lamina, further reconfirming the role in leaf development. Together, our data suggests that PpSCR1 is involved in the leaf blade and mid-vein development of moss and that its role in the regulation of cell division and proliferation is ancient and conserved among flowering plants and mosses.
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Affiliation(s)
- Boominathan Mohanasundaram
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Currently at Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Shirsa Palit
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Currently at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Amey J Bhide
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Madhusmita Pala
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Kanishka Rajoria
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Payal Girigosavi
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Currently at National AIDS Research Institute, Pune, Maharashtra, India
| | - Anjan K Banerjee
- Indian Institute of Science Education and Research (IISER-Pune), Biology Division, Dr Homi Bhabha Road, Pune, 411008, Maharashtra, India.
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4
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Flores-Sandoval E, Nishihama R, Bowman JL. Hormonal and genetic control of pluripotency in bryophyte model systems. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102486. [PMID: 38041967 DOI: 10.1016/j.pbi.2023.102486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023]
Abstract
Land plant meristems are reservoirs of pluripotent stem cells where new tissues emerge, grow and eventually differentiate into specific cell identities. Compared to algae, where cells are produced in two-dimensional tissues via tip or marginal growth, land plants have meristems that allow three-dimensional growth for successful exploration of the terrestrial environment. In land plants, meristem maintenance leads to indeterminate growth and the production of new meristems leads to branching or regeneration via reprogramming of wounded somatic cells. Emerging model systems in the haploid dominant and monophyletic bryophytes are allowing comparative analyses of meristem gene regulatory networks to address whether all plants use common or diverse programs to organise, maintain, and regenerate meristems. In this piece we aim to discuss recent advances in genetic and hormonal control of bryophyte meristems and possible convergence or discrepancies in an exciting and emerging field in plant biology.
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Affiliation(s)
- Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne, Vic, 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Vic, 3800, Australia.
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Vic, 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Vic, 3800, Australia
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5
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Takahashi G, Kiyosue T, Hirakawa Y. Control of stem cell behavior by CLE-JINGASA signaling in the shoot apical meristem in Marchantia polymorpha. Curr Biol 2023; 33:5121-5131.e6. [PMID: 37977139 DOI: 10.1016/j.cub.2023.10.054] [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] [Received: 05/19/2023] [Revised: 09/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Land plants undergo indeterminate growth by the activity of meristems in both gametophyte (haploid) and sporophyte (diploid) generations. In the sporophyte of the flowering plant Arabidopsis thaliana, the apical meristems are located at the shoot and root tips in which a number of regulatory gene homologs are shared for their development, implying deep evolutionary origins. However, little is known about their functional conservation with gametophytic meristems in distantly related land plants such as bryophytes, even though genomic studies have revealed that the subfamily-level diversity of regulatory genes is mostly conserved throughout land plants. Here, we show that a NAM/ATAF/CUC (NAC) domain transcription factor, JINGASA (MpJIN), acts downstream of CLAVATA3 (CLV3)/ESR-related (CLE) peptide signaling and controls stem cell behavior in the gametophytic shoot apical meristem of the liverwort Marchantia polymorpha. In the meristem, strong MpJIN expression was associated with the periclinal cell division at the periphery of the stem cell zone (SCZ), whereas faint MpJIN expression was found at the center of the SCZ. Time course observation indicates that the MpJIN-negative cells are lost from the SCZ and respecified de novo at two separate positions during the dichotomous branching event. Consistently, the induction of MpJIN results in ectopic periclinal cell division in the SCZ and meristem termination. Based on the comparative expression data, we speculate that the function of JIN/FEZ subfamily genes was shared among the shoot apical meristems in the gametophyte and sporophyte generations in early land plants but was lost in certain lineages, including the flowering plant A. thaliana.
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Affiliation(s)
- Go Takahashi
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan
| | - Tomohiro Kiyosue
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan
| | - Yuki Hirakawa
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan.
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6
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Pietrykowska H, Alisha A, Aggarwal B, Watanabe Y, Ohtani M, Jarmolowski A, Sierocka I, Szweykowska-Kulinska Z. Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development. PLANT MOLECULAR BIOLOGY 2023; 113:121-142. [PMID: 37991688 PMCID: PMC10721683 DOI: 10.1007/s11103-023-01392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023]
Abstract
A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.
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Affiliation(s)
- Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Alisha Alisha
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Kanagawa, Japan
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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7
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Husbands AY, Feller A, Aggarwal V, Dresden CE, Holub AS, Ha T, Timmermans MCP. The START domain potentiates HD-ZIPIII transcriptional activity. THE PLANT CELL 2023; 35:2332-2348. [PMID: 36861320 DOI: 10.1093/plcell/koad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
The CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factors (TFs) were repeatedly deployed over 725 million years of evolution to regulate central developmental innovations. The START domain of this pivotal class of developmental regulators was recognized over 20 years ago, but its putative ligands and functional contributions remain unknown. Here, we demonstrate that the START domain promotes HD-ZIPIII TF homodimerization and increases transcriptional potency. Effects on transcriptional output can be ported onto heterologous TFs, consistent with principles of evolution via domain capture. We also show the START domain binds several species of phospholipids, and that mutations in conserved residues perturbing ligand binding and/or its downstream conformational readout abolish HD-ZIPIII DNA-binding competence. Our data present a model in which the START domain potentiates transcriptional activity and uses ligand-induced conformational change to render HD-ZIPIII dimers competent to bind DNA. These findings resolve a long-standing mystery in plant development and highlight the flexible and diverse regulatory potential coded within this widely distributed evolutionary module.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
| | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Courtney E Dresden
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
- Molecular, Cellular, and Developmental Biology (MCDB), The Ohio State University, Columbus, OH 43215, USA
| | - Ashton S Holub
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
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8
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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9
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Bowman JL. The origin of a land flora. NATURE PLANTS 2022; 8:1352-1369. [PMID: 36550365 DOI: 10.1038/s41477-022-01283-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Victoria, Australia.
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10
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Ge Y, Gao Y, Jiao Y, Wang Y. A conserved module in the formation of moss midribs and seed plant axillary meristems. SCIENCE ADVANCES 2022; 8:eadd7275. [PMID: 36399581 PMCID: PMC9674282 DOI: 10.1126/sciadv.add7275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Different evolutionary lineages have evolved distinct characteristic body plans and anatomical structures, but their origins are largely elusive. For example, seed plants evolve axillary meristems to enable lateral branching. In moss, the phyllid (leaf) midrib containing specialized cells is responsible for water conduction and support. Midribs function like vascular tissues in flowering plants but may have risen from a different evolutionary path. Here, we demonstrate that midrib formation in the model moss Physcomitrium patens is regulated by orthologs of Arabidopsis LATERAL SUPPRESSOR (LAS), a key regulator of axillary meristem initiation. Midribs are missing in loss-of-function mutants, and ectopic formation of midrib-like structures is induced in overexpression lines. Furthermore, the PpLAS/AtLAS genes have conserved functions in the promotion of cell division in both lineages, which alleviates phenotypes in both Physcomitrium and Arabidopsis las mutants. Our results show that a conserved regulatory module is reused in divergent developmental programs, water-conducting and supporting tissues in moss, and axillary meristem initiation in seed plants.
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Affiliation(s)
- Yanhua Ge
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Landberg K, Lopez‐Obando M, Sanchez Vera V, Sundberg E, Thelander M. MS1/MMD1 homologues in the moss Physcomitrium patens are required for male and female gametogenesis. THE NEW PHYTOLOGIST 2022; 236:512-524. [PMID: 35775827 PMCID: PMC9796955 DOI: 10.1111/nph.18352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The Arabidopsis Plant HomeoDomain (PHD) proteins AtMS1 and AtMMD1 provide chromatin-mediated transcriptional regulation essential for tapetum-dependent pollen formation. This pollen-based male gametogenesis is a derived trait of seed plants. Male gametogenesis in the common ancestors of land plants is instead likely to have been reminiscent of that in extant bryophytes where flagellated sperms are produced by an elaborate gametophyte generation. Still, also bryophytes possess MS1/MMD1-related PHD proteins. We addressed the function of two MS1/MMD1-homologues in the bryophyte model moss Physcomitrium patens by the generation and analysis of reporter and loss-of-function lines. The two genes are together essential for both male and female fertility by providing functions in the gamete-producing inner cells of antheridia and archegonia. They are furthermore expressed in the diploid sporophyte generation suggesting a function during sporogenesis, a process proposed related by descent to pollen formation in angiosperms. We propose that the moss MS1/MMD1-related regulatory network required for completion of male and female gametogenesis, and possibly for sporogenesis, represent a heritage from ancestral land plants.
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Affiliation(s)
- Katarina Landberg
- Department of Plant BiologyThe Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural SciencesPO Box 7080SE‐75007UppsalaSweden
| | - Mauricio Lopez‐Obando
- Department of Plant BiologyThe Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural SciencesPO Box 7080SE‐75007UppsalaSweden
| | - Victoria Sanchez Vera
- Department of Plant BiologyThe Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural SciencesPO Box 7080SE‐75007UppsalaSweden
| | - Eva Sundberg
- Department of Plant BiologyThe Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural SciencesPO Box 7080SE‐75007UppsalaSweden
| | - Mattias Thelander
- Department of Plant BiologyThe Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural SciencesPO Box 7080SE‐75007UppsalaSweden
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12
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Wang D, Gong Y, Li Y, Nie S. Genome-wide analysis of the homeodomain-leucine zipper family in Lotus japonicus and the overexpression of LjHDZ7 in Arabidopsis for salt tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:955199. [PMID: 36186025 PMCID: PMC9515785 DOI: 10.3389/fpls.2022.955199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) family participates in plant growth, development, and stress responses. Here, 40 HD-Zip transcription factors of Lotus japonicus were identified and gave an overview of the phylogeny and gene structures. The expression pattern of these candidate genes was determined in different organs and their response to abiotic stresses, including cold, heat, polyethylene glycol and salinity. The expression of the LjHDZ7 was strongly induced by abiotic stress, especially salt stress. Subsequently, LjHDZ7 gene was overexpressed in Arabidopsis. The transgenic plants grew obviously better than Col-0 plants under salt stress. Furthermore, LjHDZ7 transgenic lines accumulated higher proline contents and showed lower electrolyte leakage and MDA contents than Col-0 plants under salt stress. Antioxidant activities of the LjHDZ7 overexpression lines leaf were significantly higher than those of the Col-0 plants under salt stress. The concentration of Na+ ion in LjHDZ7 overexpression lines was significantly lower than that of Col-0 in leaf and root parts. The concentration of K+ ion in LjHDZ7 overexpression lines was significantly higher than that of Col-0 in the leaf parts. Therefore, these results showed that overexpression of LjHDZ7 increased resistance to salt stress in transgenic Arabidopsis plants, and certain genes of this family can be used as valuable tools for improving abiotic stresses.
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13
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Fouracre JP, Harrison CJ. How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants. PLANT PHYSIOLOGY 2022; 190:100-112. [PMID: 35771646 PMCID: PMC9434304 DOI: 10.1093/plphys/kiac313] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Land plant life cycles are separated into distinct haploid gametophyte and diploid sporophyte stages. Indeterminate apical growth evolved independently in bryophyte (moss, liverwort, and hornwort) and fern gametophytes, and tracheophyte (vascular plant) sporophytes. The extent to which apical growth in tracheophytes co-opted conserved gametophytic gene networks, or exploited ancestral sporophytic networks, is a long-standing question in plant evolution. The recent phylogenetic confirmation of bryophytes and tracheophytes as sister groups has led to a reassessment of the nature of the ancestral land plant. Here, we review developmental genetic studies of apical regulators and speculate on their likely evolutionary history.
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Affiliation(s)
- Jim P Fouracre
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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14
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Woudenberg S, Renema J, Tomescu AMF, De Rybel B, Weijers D. Deep origin and gradual evolution of transporting tissues: Perspectives from across the land plants. PLANT PHYSIOLOGY 2022; 190:85-99. [PMID: 35904762 PMCID: PMC9434249 DOI: 10.1093/plphys/kiac304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/08/2022] [Indexed: 05/31/2023]
Abstract
The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant-soil and plant-air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.
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Affiliation(s)
| | | | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University–Humboldt, Arcata, California 95521, USA
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15
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Ahmad S, Chen Y, Shah AZ, Wang H, Xi C, Zhu H, Ge L. The Homeodomain-Leucine Zipper Genes Family Regulates the Jinggangmycin Mediated Immune Response of Oryza sativa to Nilaparvata lugens, and Laodelphax striatellus. Bioengineering (Basel) 2022; 9:bioengineering9080398. [PMID: 36004924 PMCID: PMC9405480 DOI: 10.3390/bioengineering9080398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/16/2022] Open
Abstract
The homeodomain-leucine zipper (HDZIP) is an important transcription factor family, instrumental not only in growth but in finetuning plant responses to environmental adversaries. Despite the plethora of literature available, the role of HDZIP genes under chewing and sucking insects remains elusive. Herein, we identified 40 OsHDZIP genes from the rice genome database. The evolutionary relationship, gene structure, conserved motifs, and chemical properties highlight the key aspects of OsHDZIP genes in rice. The OsHDZIP family is divided into a further four subfamilies (i.e., HDZIP I, HDZIP II, HDZIP III, and HDZIP IV). Moreover, the protein–protein interaction and Gene Ontology (GO) analysis showed that OsHDZIP genes regulate plant growth and response to various environmental stimuli. Various microRNA (miRNA) families targeted HDZIP III subfamily genes. The microarray data analysis showed that OsHDZIP was expressed in almost all tested tissues. Additionally, the differential expression patterns of the OsHDZIP genes were found under salinity stress and hormonal treatments, whereas under brown planthopper (BPH), striped stem borer (SSB), and rice leaf folder (RLF), only OsHDZIP3, OsHDZIP4, OsHDZIP40, OsHDZIP10, and OsHDZIP20 displayed expression. The qRT-PCR analysis further validated the expression of OsHDZIP20, OsHDZIP40, and OsHDZIP10 under BPH, small brown planthopper (SBPH) infestations, and jinggangmycin (JGM) spraying applications. Our results provide detailed knowledge of the OsHDZIP gene family resistance in rice plants and will facilitate the development of stress-resilient cultivars, particularly against chewing and sucking insect pests.
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16
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Nakayama H, Leichty AR, Sinha NR. Molecular mechanisms underlying leaf development, morphological diversification, and beyond. THE PLANT CELL 2022; 34:2534-2548. [PMID: 35441681 PMCID: PMC9252486 DOI: 10.1093/plcell/koac118] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/13/2022] [Indexed: 05/13/2023]
Abstract
The basic mechanisms of leaf development have been revealed through a combination of genetics and intense analyses in select model species. The genetic basis for diversity in leaf morphology seen in nature is also being unraveled through recent advances in techniques and technologies related to genomics and transcriptomics, which have had a major impact on these comparative studies. However, this has led to the emergence of new unresolved questions about the mechanisms that generate the diversity of leaf form. Here, we provide a review of the current knowledge of the fundamental molecular genetic mechanisms underlying leaf development with an emphasis on natural variation and conserved gene regulatory networks involved in leaf development. Beyond that, we discuss open questions/enigmas in the area of leaf development, how recent technologies can best be deployed to generate a unified understanding of leaf diversity and its evolution, and what untapped fields lie ahead.
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Affiliation(s)
- Hokuto Nakayama
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Aaron R Leichty
- Department of Plant Biology, University of California Davis, Davis, California 95616, USA
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17
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Lopez‐Obando M, Landberg K, Sundberg E, Thelander M. Dependence on clade II bHLH transcription factors for nursing of haploid products by tapetal-like cells is conserved between moss sporangia and angiosperm anthers. THE NEW PHYTOLOGIST 2022; 235:718-731. [PMID: 35037245 PMCID: PMC9306660 DOI: 10.1111/nph.17972] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/28/2021] [Indexed: 05/16/2023]
Abstract
Clade II basic helix-loop-helix transcription factors (bHLH TFs) are essential for pollen production and tapetal nursing functions in angiosperm anthers. As pollen has been suggested to be related to bryophyte spores by descent, we characterized two Physcomitrium (Physcomitrella) patens clade II bHLH TFs (PpbHLH092 and PpbHLH098), to test if regulation of sporogenous cells and the nursing cells surrounding them is conserved between angiosperm anthers and bryophyte sporangia. We made CRISPR-Cas9 reporter and loss-of-function lines to address the function of PpbHLH092/098. We sectioned and analyzed WT and mutant sporophytes for a comprehensive stage-by-stage comparison of sporangium development. Spore precursors in the P. patens sporangium are surrounded by nursing cells showing striking similarities to tapetal cells in angiosperms. Moss clade II bHLH TFs are essential for the differentiation of these tapetal-like cells and for the production of functional spores. Clade II bHLH TFs provide a conserved role in controlling the sporophytic somatic cells surrounding and nursing the sporogenous cells in both moss sporangia and angiosperm anthers. This supports the hypothesis that such nursing functions in mosses and angiosperms, lineages separated by c. 450 million years, are related by descent.
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Affiliation(s)
- Mauricio Lopez‐Obando
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
- VEDAS Corporación de Investigación e Innovación (VEDASCII)Cl 8 B 65‐261 050024MedellínColombia
| | - Katarina Landberg
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
| | - Eva Sundberg
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
| | - Mattias Thelander
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
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18
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Oliver C, Martinez G. Accumulation dynamics of ARGONAUTE proteins during meiosis in Arabidopsis. PLANT REPRODUCTION 2022; 35:153-160. [PMID: 34812935 PMCID: PMC9110482 DOI: 10.1007/s00497-021-00434-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Meiosis is a specialized cell division that is key for reproduction and genetic diversity in sexually reproducing plants. Recently, different RNA silencing pathways have been proposed to carry a specific activity during meiosis, but the pathways involved during this process remain unclear. Here, we explored the subcellular localization of different ARGONAUTE (AGO) proteins, the main effectors of RNA silencing, during male meiosis in Arabidopsis thaliana using immunolocalizations with commercially available antibodies. We detected the presence of AGO proteins associated with posttranscriptional gene silencing (AGO1, 2, and 5) in the cytoplasm and the nucleus, while AGOs associated with transcriptional gene silencing (AGO4 and 9) localized exclusively in the nucleus. These results indicate that the localization of different AGOs correlates with their predicted roles at the transcriptional and posttranscriptional levels and provide an overview of their timing and potential role during meiosis.
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Affiliation(s)
- Cecilia Oliver
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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19
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Hata Y, Kyozuka J. Fundamental mechanisms of the stem cell regulation in land plants: lesson from shoot apical cells in bryophytes. PLANT MOLECULAR BIOLOGY 2021; 107:213-225. [PMID: 33609252 PMCID: PMC8648652 DOI: 10.1007/s11103-021-01126-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/01/2021] [Indexed: 05/02/2023]
Abstract
This review compares the molecular mechanisms of stem cell control in the shoot apical meristems of mosses and angiosperms and reveals the conserved features and evolution of plant stem cells. The establishment and maintenance of pluripotent stem cells in the shoot apical meristem (SAM) are key developmental processes in land plants including the most basal, bryophytes. Bryophytes, such as Physcomitrium (Physcomitrella) patens and Marchantia polymorpha, are emerging as attractive model species to study the conserved features and evolutionary processes in the mechanisms controlling stem cells. Recent studies using these model bryophyte species have started to uncover the similarities and differences in stem cell regulation between bryophytes and angiosperms. In this review, we summarize findings on stem cell function and its regulation focusing on different aspects including hormonal, genetic, and epigenetic control. Stem cell regulation through auxin, cytokinin, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling and chromatin modification by Polycomb Repressive Complex 2 (PRC2) and PRC1 is well conserved. Several transcription factors crucial for SAM regulation in angiosperms are not involved in the regulation of the SAM in mosses, but similarities also exist. These findings provide insights into the evolutionary trajectory of the SAM and the fundamental mechanisms involved in stem cell regulation that are conserved across land plants.
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Affiliation(s)
- Yuki Hata
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan.
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20
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Yadav A, Kumar S, Verma R, Lata C, Sanyal I, Rai SP. microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2471-2485. [PMID: 34924705 PMCID: PMC8639965 DOI: 10.1007/s12298-021-01096-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.
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Affiliation(s)
- Ankita Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Sanoj Kumar
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005 India
| | - Rita Verma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067 India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shashi Pandey Rai
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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21
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Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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22
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Lin W, Wang Y, Coudert Y, Kierzkowski D. Leaf Morphogenesis: Insights From the Moss Physcomitrium patens. FRONTIERS IN PLANT SCIENCE 2021; 12:736212. [PMID: 34630486 PMCID: PMC8494982 DOI: 10.3389/fpls.2021.736212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/02/2021] [Indexed: 05/17/2023]
Abstract
Specialized photosynthetic organs have appeared several times independently during the evolution of land plants. Phyllids, the leaf-like organs of bryophytes such as mosses or leafy liverworts, display a simple morphology, with a small number of cells and cell types and lack typical vascular tissue which contrasts greatly with flowering plants. Despite this, the leaf structures of these two plant types share many morphological characteristics. In this review, we summarize the current understanding of leaf morphogenesis in the model moss Physcomitrium patens, focusing on the underlying cellular patterns and molecular regulatory mechanisms. We discuss this knowledge in an evolutionary context and identify parallels between moss and flowering plant leaf development. Finally, we propose potential research directions that may help to answer fundamental questions in plant development using moss leaves as a model system.
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Affiliation(s)
- Wenye Lin
- IRBV, Department of Biological Sciences, University of Montréal, Montréal, Montréal, QC, Canada
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, CNRS, INRA, Université Claude Bernard Lyon 1, INRIA, Lyon, France
| | - Daniel Kierzkowski
- IRBV, Department of Biological Sciences, University of Montréal, Montréal, Montréal, QC, Canada
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23
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Romani F, Moreno JE. Molecular mechanisms involved in functional macroevolution of plant transcription factors. THE NEW PHYTOLOGIST 2021; 230:1345-1353. [PMID: 33368298 DOI: 10.1111/nph.17161] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/17/2020] [Indexed: 05/04/2023]
Abstract
Transcription factors (TFs) are key components of the transcriptional regulation machinery. In plants, they accompanied the evolution from unicellular aquatic algae to complex flowering plants that dominate the land environment. The adaptations of the body plan and physiological responses required changes in the biological functions of TFs. Some ancestral gene regulatory networks are highly conserved, while others evolved more recently and only exist in particular lineages. The recent emergence of novel model organisms provided the opportunity for comparative studies, producing new insights to infer these evolutionary trajectories. In this review, we comprehensively revisit the recent literature on TFs of nonseed plants and algae, focusing on the molecular mechanisms driving their functional evolution. We discuss the particular contribution of changes in DNA-binding specificity, protein-protein interactions and cis-regulatory elements to gene regulatory networks. Current advances have shown that these evolutionary processes were shaped by changes in TF expression pattern, not through great innovation in TF protein sequences. We propose that the role of TFs associated with environmental and developmental regulation was unevenly conserved during land plant evolution.
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Affiliation(s)
- Facundo Romani
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral - CONICET, Colectora RN 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Javier E Moreno
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral - CONICET, Colectora RN 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
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24
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Hu G, Lei Y, Liu J, Hao M, Zhang Z, Tang Y, Chen A, Wu J. The ghr-miR164 and GhNAC100 modulate cotton plant resistance against Verticillium dahlia. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110438. [PMID: 32081275 DOI: 10.1101/440826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 05/28/2023]
Abstract
MicroRNAs (miRNAs) participate in plant development and defence through post-transcriptional regulation of the target genes. However, few miRNAs were reported to regulate cotton plant disease resistance. Here, we characterized the cotton miR164-NAC100 module in the later induction stage response of the plant to Verticillium dahliae infection. The results of GUS fusing reporter and transcript identity showed that ghr-miR164 can directly cleave the mRNA of GhNAC100 in the post-transcriptional process. The ghr-miR164 positively regulated the cotton plant resistance to V. dahliae according to analyses of its over-expression and knockdown. In link with results, the knockdown of GhNAC100 increased the plant resistance to V. dahliae. Based on LUC reporter, expression analyses and yeast one-hybrid (Y1H) assays, GhNAC100 bound to the CGTA-box of GhPR3 promoter and repressed its expression, negatively regulating plant disease resistance. These results showed that the ghr-miR164 and GhNAC100 module fine-tunes plant defence through the post-transcriptional regulation, which documented that miRNAs play important roles in plant resistance to vascular disease.
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Affiliation(s)
- Guang Hu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China
| | - Yu Lei
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfen Liu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengyan Hao
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhennan Zhang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ye Tang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aiming Chen
- The Key Laboratory for the Creation of Cotton Varieties in the Northwest, Ministry of Agriculture, Join Hope Seeds CO. Ltd, Changji, Xinjiang, 831100, China
| | - Jiahe Wu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China.
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25
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26
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Abstract
Land plants evolved from an ancestral alga from which they inherited developmental and physiological characters. A key innovation of land plants is a life cycle with an alternation of generations, with both haploid gametophyte and diploid sporophyte generations having complex multicellular bodies. The origins of the developmental genetic programs patterning these bodies, whether inherited from an algal ancestor or evolved de novo, and whether programs were co-opted between generations, are largely open questions. We first provide a framework for land plant evolution and co-option of developmental regulatory pathways and then examine two cases in more detail.
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27
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Plackett AR, Conway SJ, Hewett Hazelton KD, Rabbinowitsch EH, Langdale JA, Di Stilio VS. LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii. eLife 2018; 7:39625. [PMID: 30355440 PMCID: PMC6200394 DOI: 10.7554/elife.39625] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/22/2018] [Indexed: 12/29/2022] Open
Abstract
During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mosses and primarily for floral meristem identity in flowering plants, may have facilitated developmental innovations during these transitions. Mapping the LEAFY evolutionary trajectory has been challenging, however, because there is no functional overlap between mosses and flowering plants, and no functional data from intervening lineages. Here, we report a transgenic analysis in the fern Ceratopteris richardii that reveals a role for LEAFY in maintaining cell divisions in the apical stem cells of both haploid and diploid phases of the lifecycle. These results support an evolutionary trajectory in which an ancestral LEAFY module that promotes cell proliferation was progressively co-opted, adapted and specialized as novel shoot developmental contexts emerged. The first plants colonized land around 500 million years ago. These plants had simple shoots with no branches, similar to the mosses that live today. Later on, some plants evolved more complex structures including branched shoots and flowers (collectively known as the “flowering plants”). Ferns are a group of plants that evolved midway between the mosses and flowering plants and have branched shoots but no flowers. The gradual transition from simple to more complex plant structures required changes to the way in which cells divide and grow within plant shoots. Whereas animals produce new cells throughout their body, most plant cells divide in areas known as meristems. All plants grow from embryos, which contain meristems that will form the roots and shoots of the mature plant. A gene called LEAFY is required for cells in moss embryos to divide. However, in flowering plants LEAFY does not carry out this role, instead it is only required to make the meristems that produce flowers. How did LEAFY transition from a general role in embryos to a more specialized role in making flowers? To address this question, Plackett, Conway et al. studied the two LEAFY genes in a fern called Ceratopteris richardii. The experiments showed that at least one of these LEAFY genes was active in the meristems of fern shoots throughout the lifespan of the plant. The shoots of ferns with less active LEAFY genes could not form the leaves seen in normal C. richardii plants. This suggests that as land plants evolved, the role of LEAFY changed from forming embryos to forming complex shoot structures. Most of our major crops are flowering plants. By understanding how the role of LEAFY has changed over the evolution of land plants, it might be possible to manipulate LEAFY genes in crop plants to alter shoot structures to better suit specific environments.
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Affiliation(s)
- Andrew Rg Plackett
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Furumizu C, Hirakawa Y, Bowman JL, Sawa S. 3D Body Evolution: Adding a New Dimension to Colonize the Land. Curr Biol 2018; 28:R838-R840. [DOI: 10.1016/j.cub.2018.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Romani F, Reinheimer R, Florent SN, Bowman JL, Moreno JE. Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. THE NEW PHYTOLOGIST 2018; 219:408-421. [PMID: 29635737 DOI: 10.1111/nph.15133] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/26/2018] [Indexed: 05/15/2023]
Abstract
Plant transition to land required several regulatory adaptations. The mechanisms behind these changes remain unknown. Since the evolution of transcription factors (TFs) families accompanied this transition, we studied the HOMEODOMAIN LEUCINE ZIPPER (HDZ) TF family known to control key developmental and environmental responses. We performed a phylogenetic and bioinformatics analysis of HDZ genes using transcriptomic and genomic datasets from a wide range of Viridiplantae species. We found evidence for the existence of HDZ genes in chlorophytes and early-divergent charophytes identifying several HDZ members belonging to the four known classes (I-IV). Furthermore, we inferred a progressive incorporation of auxiliary motifs. Interestingly, most of the structural features were already present in ancient lineages. Our phylogenetic analysis inferred that the origin of classes I, III, and IV is monophyletic in land plants in respect to charophytes. However, class IIHDZ genes have two conserved lineages in charophytes and mosses that differ in the CPSCE motif. Our results indicate that the HDZ family was already present in green algae. Later, the HDZ family expanded accompanying critical plant traits. Once on land, the HDZ family experienced multiple duplication events that promoted fundamental neo- and subfunctionalizations for terrestrial life.
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Affiliation(s)
- Facundo Romani
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No. 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Renata Reinheimer
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Ciencias Agrarias, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No. 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Stevie N Florent
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Javier E Moreno
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No. 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
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Augstein F, Carlsbecker A. Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:1410. [PMID: 30319672 PMCID: PMC6167918 DOI: 10.3389/fpls.2018.01410] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.
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Hou Y, Zhai L, Li X, Xue Y, Wang J, Yang P, Cao C, Li H, Cui Y, Bian S. Comparative Analysis of Fruit Ripening-Related miRNAs and Their Targets in Blueberry Using Small RNA and Degradome Sequencing. Int J Mol Sci 2017; 18:ijms18122767. [PMID: 29257112 PMCID: PMC5751366 DOI: 10.3390/ijms18122767] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) play vital roles in the regulation of fruit development and ripening. Blueberry is an important small berry fruit crop with economical and nutritional value. However, nothing is known about the miRNAs and their targets involved in blueberry fruit ripening. In this study, using high-throughput sequencing of small RNAs, 84 known miRNAs belonging to 28 families and 16 novel miRNAs were identified in white fruit (WF) and blue fruit (BF) libraries, which represent fruit ripening onset and in progress, respectively. Among them, 41 miRNAs were shown to be differentially expressed during fruit maturation, and 16 miRNAs representing 16 families were further chosen to validate the sRNA sequencing data by stem-loop qRT-PCR. Meanwhile, 178 targets were identified for 41 known and 7 novel miRNAs in WF and BF libraries using degradome sequencing, and targets of miR160 were validated using RLM-RACE (RNA Ligase-Mediated (RLM)-Rapid Amplification of cDNA Ends) approach. Moreover, the expression patterns of 6 miRNAs and their targets were examined during fruit development and ripening. Finally, integrative analysis of miRNAs and their targets revealed a complex miRNA-mRNA regulatory network involving a wide variety of biological processes. The findings will facilitate future investigations of the miRNA-mediated mechanisms that regulate fruit development and ripening in blueberry.
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Affiliation(s)
- Yanming Hou
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Yu Xue
- College of Life Sciences, Jilin University, Changchun 130012, China.
| | - Jingjing Wang
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Pengjie Yang
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Chunmei Cao
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Hongxue Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada.
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun 130062, China.
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Jill Harrison C. Development and genetics in the evolution of land plant body plans. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150490. [PMID: 27994131 PMCID: PMC5182422 DOI: 10.1098/rstb.2015.0490] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/22/2022] Open
Abstract
The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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Li X, Xie X, Li J, Cui Y, Hou Y, Zhai L, Wang X, Fu Y, Liu R, Bian S. Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s. BMC PLANT BIOLOGY 2017; 17:32. [PMID: 28143404 PMCID: PMC5286673 DOI: 10.1186/s12870-017-0983-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/23/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. RESULTS We identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity. CONCLUSION This study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or under abiotic stresses.
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Affiliation(s)
- Xuyan Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Xin Xie
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Ji Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
| | - Yanming Hou
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Xiao Wang
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Yanli Fu
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Ranran Liu
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, Jilin, China.
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34
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Ramachandran P, Carlsbecker A, Etchells JP. Class III HD-ZIPs govern vascular cell fate: an HD view on patterning and differentiation. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:55-69. [PMID: 27794018 DOI: 10.1093/jxb/erw370] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant vasculature is required for the transport of water and solutes throughout the plant body. It is constituted of xylem, specialized for transport of water, and phloem, that transports photosynthates. These two differentiated tissues are specified early in development and arise from divisions in the procambium, which is the vascular meristem during primary growth. During secondary growth, the xylem and phloem are further expanded via differentiation of cells derived from divisions in the cambium. Almost all of the developmental fate decisions in this process, including vascular specification, patterning, and differentiation, are regulated by transcription factors belonging to the class III homeodomain-leucine zipper (HD-ZIP III) family. This review draws together the literature describing the roles that these genes play in vascular development, looking at how HD-ZIP IIIs are regulated, and how they in turn influence other regulators of vascular development. Themes covered vary, from interactions between HD-ZIP IIIs and auxin, cytokinin, and brassinosteroids, to the requirement for exquisite spatial and temporal regulation of HD-ZIP III expression through miRNA-mediated post-transcriptional regulation, and interactions with other transcription factors. The literature described places the HD-ZIP III family at the centre of a complex network required for initiating and maintaining plant vascular tissues.
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Affiliation(s)
- Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls väg 24E, SE-756 51 Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls väg 24E, SE-756 51 Uppsala, Sweden
| | - J Peter Etchells
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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35
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Abstract
The life cycles of eukaryotes alternate between haploid and diploid phases, which are initiated by meiosis and gamete fusion, respectively. In both ascomycete and basidiomycete fungi and chlorophyte algae, the haploid-to-diploid transition is regulated by a pair of paralogous homeodomain protein encoding genes. That a common genetic program controls the haploid-to-diploid transition in phylogenetically disparate eukaryotic lineages suggests this may be the ancestral function for homeodomain proteins. Multicellularity has evolved independently in many eukaryotic lineages in either one or both phases of the life cycle. Organisms, such as land plants, exhibiting a life cycle whereby multicellular bodies develop in both the haploid and diploid phases are often referred to as possessing an alternation of generations. We review recent progress on understanding the genetic basis for the land plant alternation of generations and highlight the roles that homeodomain-encoding genes may have played in the evolution of complex multicellularity in this lineage.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
- Department of Plant Biology, University of California, Davis, California 95616
| | - Keiko Sakakibara
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Chihiro Furumizu
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
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36
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Chitwood DH, Irish VF. A renaissance in plant development. Dev Biol 2016; 419:4-6. [PMID: 27637462 DOI: 10.1016/j.ydbio.2016.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Vivian F Irish
- Department of Molecular, Cellular and Developmental Biology, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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37
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Vasco A, Smalls TL, Graham SW, Cooper ED, Wong GKS, Stevenson DW, Moran RC, Ambrose BA. Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes. THE NEW PHYTOLOGIST 2016; 212:745-758. [PMID: 27385116 DOI: 10.1111/nph.14075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/23/2016] [Indexed: 05/06/2023]
Abstract
Despite the extraordinary significance leaves have for life on Earth, their origin and development remain vigorously debated. More than a century of paleobotanical, morphological, and phylogenetic research has still not resolved fundamental questions about leaves. Developmental genetic data are sparse in ferns, and comparative studies of lycophytes and seed plants have reached opposing conclusions on the conservation of a leaf developmental program. We performed phylogenetic and expression analyses of a leaf developmental regulator (Class III HD-Zip genes; C3HDZs) spanning lycophytes and ferns. We show that a duplication and neofunctionalization of C3HDZs probably occurred in the ancestor of euphyllophytes, and that there is a common leaf developmental mechanism conserved between ferns and seed plants. We show C3HDZ expression in lycophyte and fern sporangia and show that C3HDZs have conserved expression patterns during initiation of lateral primordia (leaves or sporangia). This expression is maintained throughout sporangium development in lycophytes and ferns and indicates an ancestral role of C3HDZs in sporangium development. We hypothesize that there is a deep homology of all leaves and that a sporangium-specific developmental program was coopted independently for the development of lycophyte and euphyllophyte leaves. This provides molecular genetic support for a paradigm shift in theories of lycophyte leaf evolution.
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Affiliation(s)
- Alejandra Vasco
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Mexico DF, 04510, Mexico
| | - Tynisha L Smalls
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
| | - Endymion D Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Robbin C Moran
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA.
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38
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Horst NA, Reski R. Alternation of generations - unravelling the underlying molecular mechanism of a 165-year-old botanical observation. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:549-51. [PMID: 27094475 DOI: 10.1111/plb.12468] [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: 03/02/2016] [Accepted: 04/15/2016] [Indexed: 05/02/2023]
Abstract
Characteristically, land plants exhibit a life cycle with an 'alternation of generations' and thus alternate between a haploid gametophyte and a diploid sporophyte. At meiosis and fertilisation the transitions between these two ontogenies take place in distinct single stem cells. The evolutionary invention of an embryo, and thus an upright multicellular sporophyte, in the ancestor of land plants formed the basis for the evolution of increasingly complex plant morphologies shaping Earth's ecosystems. Recent research employing the moss Physcomitrella patens revealed the homeotic gene BELL1 as a master regulator of the gametophyte-to-sporophyte transition. Here, we discuss these findings in the context of classical botanical observations.
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Affiliation(s)
- N A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - R Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany
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