1
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Sessa G, Carabelli M, Sassi M. The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development. Int J Mol Sci 2024; 25:5657. [PMID: 38891845 PMCID: PMC11171833 DOI: 10.3390/ijms25115657] [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: 04/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.
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Affiliation(s)
| | | | - Massimiliano Sassi
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy; (G.S.); (M.C.)
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2
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Li S, Wei L, Gao Q, Xu M, Wang Y, Lin Z, Holford P, Chen ZH, Zhang L. Molecular and phylogenetic evidence of parallel expansion of anion channels in plants. PLANT PHYSIOLOGY 2024; 194:2533-2548. [PMID: 38142233 DOI: 10.1093/plphys/kiad687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Aluminum-activated malate transporters (ALMTs) and slow anion channels (SLACs) are important in various physiological processes in plants, including stomatal regulation, nutrient uptake, and in response to abiotic stress such as aluminum toxicity. To understand their evolutionary history and functional divergence, we conducted phylogenetic and expression analyses of ALMTs and SLACs in green plants. Our findings from phylogenetic studies indicate that ALMTs and SLACs may have originated from green algae and red algae, respectively. The ALMTs of early land plants and charophytes formed a monophyletic clade consisting of three subgroups. A single duplication event of ALMTs was identified in vascular plants and subsequent duplications into six clades occurred in angiosperms, including an identified clade, 1-1. The ALMTs experienced gene number losses in clades 1-1 and 2-1 and expansions in clades 1-2 and 2-2b. Interestingly, the expansion of clade 1-2 was also associated with higher expression levels compared to genes in clades that experienced apparent loss. SLACs first diversified in bryophytes, followed by duplication in vascular plants, giving rise to three distinct clades (I, II, and III), and clade II potentially associated with stomatal control in seed plants. SLACs show losses in clades II and III without substantial expansion in clade I. Additionally, ALMT clade 2-2 and SLAC clade III contain genes specifically expressed in reproductive organs and roots in angiosperms, lycophytes, and mosses, indicating neofunctionalization. In summary, our study demonstrates the evolutionary complexity of ALMTs and SLACs, highlighting their crucial role in the adaptation and diversification of vascular plants.
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Affiliation(s)
- Shanshan Li
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lanlan Wei
- College of Life Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Min Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St.Louis, MO 63104, USA
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Liangsheng Zhang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
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3
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Bolhuis DL, Dixit R, Slep KC. Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain. PLoS One 2023; 18:e0290024. [PMID: 38157339 PMCID: PMC10756542 DOI: 10.1371/journal.pone.0290024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/01/2023] [Indexed: 01/03/2024] Open
Abstract
Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.
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Affiliation(s)
- Derek L. Bolhuis
- Program in Molecular and Cellular Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ram Dixit
- Department of Biology and Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Kevin C. Slep
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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4
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Mueller KK, Pfeifer L, Schuldt L, Szövényi P, de Vries S, de Vries J, Johnson KL, Classen B. Fern cell walls and the evolution of arabinogalactan proteins in streptophytes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:875-894. [PMID: 36891885 DOI: 10.1111/tpj.16178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 05/27/2023]
Abstract
Significant changes have occurred in plant cell wall composition during evolution and diversification of tracheophytes. As the sister lineage to seed plants, knowledge on the cell wall of ferns is key to track evolutionary changes across tracheophytes and to understand seed plant-specific evolutionary innovations. Fern cell wall composition is not fully understood, including limited knowledge of glycoproteins such as the fern arabinogalactan proteins (AGPs). Here, we characterize the AGPs from the leptosporangiate fern genera Azolla, Salvinia, and Ceratopteris. The carbohydrate moiety of seed plant AGPs consists of a galactan backbone including mainly 1,3- and 1,3,6-linked pyranosidic galactose, which is conserved across the investigated fern AGPs. Yet, unlike AGPs of angiosperms, those of ferns contained the unusual sugar 3-O-methylrhamnose. Besides terminal furanosidic arabinose, Ara (Araf), the main linkage type of Araf in the ferns was 1,2-linked Araf, whereas in seed plants 1,5-linked Araf is often dominating. Antibodies directed against carbohydrate epitopes of AGPs supported the structural differences between AGPs of ferns and seed plants. Comparison of AGP linkage types across the streptophyte lineage showed that angiosperms have rather conserved monosaccharide linkage types; by contrast bryophytes, ferns, and gymnosperms showed more variability. Phylogenetic analyses of glycosyltransferases involved in AGP biosynthesis and bioinformatic search for AGP protein backbones revealed a versatile genetic toolkit for AGP complexity in ferns. Our data reveal important differences across AGP diversity of which the functional significance is unknown. This diversity sheds light on the evolution of the hallmark feature of tracheophytes: their elaborate cell walls.
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Affiliation(s)
- Kim-Kristine Mueller
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lukas Pfeifer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lina Schuldt
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zurich, Switzerland
- Zurich-Basel Plant Science Center (PSC), ETH Zürich, Tannenstrasse 1, 8092, Zürich, Switzerland
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtsr. 1, 37077, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Kim L Johnson
- Department of Animal, Plant and Soil Science, La Trobe Institute for Agriculture & Food, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Birgit Classen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
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5
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Duarte GT, Volkova PY, Fiengo Perez F, Horemans N. Chronic Ionizing Radiation of Plants: An Evolutionary Factor from Direct Damage to Non-Target Effects. PLANTS (BASEL, SWITZERLAND) 2023; 12:1178. [PMID: 36904038 PMCID: PMC10005729 DOI: 10.3390/plants12051178] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In present times, the levels of ionizing radiation (IR) on the surface of Earth are relatively low, posing no high challenges for the survival of contemporary life forms. IR derives from natural sources and naturally occurring radioactive materials (NORM), the nuclear industry, medical applications, and as a result of radiation disasters or nuclear tests. In the current review, we discuss modern sources of radioactivity, its direct and indirect effects on different plant species, and the scope of the radiation protection of plants. We present an overview of the molecular mechanisms of radiation responses in plants, which leads to a tempting conjecture of the evolutionary role of IR as a limiting factor for land colonization and plant diversification rates. The hypothesis-driven analysis of available plant genomic data suggests an overall DNA repair gene families' depletion in land plants compared to ancestral groups, which overlaps with a decrease in levels of radiation exposure on the surface of Earth millions of years ago. The potential contribution of chronic IR as an evolutionary factor in combination with other environmental factors is discussed.
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Affiliation(s)
| | | | | | - Nele Horemans
- Belgian Nuclear Research Centre—SCK CEN, 2400 Mol, Belgium
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
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6
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Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun 2023; 14:986. [PMID: 36813788 PMCID: PMC9946954 DOI: 10.1038/s41467-023-36517-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zhong Chen
- Amoeba Education Hub, 1 West Coast Road, 128020, Singapore, Singapore
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Marius Arend
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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7
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García I, Chouaia B, Llabrés M, Simeoni M. Exploring the expressiveness of abstract metabolic networks. PLoS One 2023; 18:e0281047. [PMID: 36758030 PMCID: PMC9910719 DOI: 10.1371/journal.pone.0281047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Metabolism is characterised by chemical reactions linked to each other, creating a complex network structure. The whole metabolic network is divided into pathways of chemical reactions, such that every pathway is a metabolic function. A simplified representation of metabolism, which we call an abstract metabolic network, is a graph in which metabolic pathways are nodes and there is an edge between two nodes if their corresponding pathways share one or more compounds. The abstract metabolic network of a given organism results in a small network that requires low computational power to be analysed and makes it a suitable model to perform a large-scale comparison of organisms' metabolism. To explore the potentials and limits of such a basic representation, we considered a comprehensive set of KEGG organisms, represented through their abstract metabolic network. We performed pairwise comparisons using graph kernel methods and analyse the results through exploratory data analysis and machine learning techniques. The results show that abstract metabolic networks discriminate macro evolutionary events, indicating that they are expressive enough to capture key steps in metabolism evolution.
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Affiliation(s)
- Irene García
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Bessem Chouaia
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
| | - Mercè Llabrés
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Marta Simeoni
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
- European Centre for Living Technology (ECLT), Venice, Italy
- * E-mail:
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8
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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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9
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Khan K, Van Aken O. The colonization of land was a likely driving force for the evolution of mitochondrial retrograde signalling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7182-7197. [PMID: 36055768 PMCID: PMC9675596 DOI: 10.1093/jxb/erac351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Most retrograde signalling research in plants was performed using Arabidopsis, so an evolutionary perspective on mitochondrial retrograde regulation (MRR) is largely missing. Here, we used phylogenetics to track the evolutionary origins of factors involved in plant MRR. In all cases, the gene families can be traced to ancestral green algae or earlier. However, the specific subfamilies containing factors involved in plant MRR in many cases arose during the transition to land. NAC transcription factors with C-terminal transmembrane domains, as observed in the key regulator ANAC017, can first be observed in non-vascular mosses, and close homologs to ANAC017 can be found in seed plants. Cyclin-dependent kinases (CDKs) are common to eukaryotes, but E-type CDKs that control MRR also diverged in conjunction with plant colonization of land. AtWRKY15 can be traced to the earliest land plants, while AtWRKY40 only arose in angiosperms and AtWRKY63 even more recently in Brassicaceae. Apetala 2 (AP2) transcription factors are traceable to algae, but the ABI4 type again only appeared in seed plants. This strongly suggests that the transition to land was a major driver for developing plant MRR pathways, while additional fine-tuning events have appeared in seed plants or later. Finally, we discuss how MRR may have contributed to meeting the specific challenges that early land plants faced during terrestrialization.
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Affiliation(s)
- Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
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10
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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11
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Abstract
The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
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12
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Zhao D, Yao Z, Zhang J, Zhang R, Mou Z, Zhang X, Li Z, Feng X, Chen S, Reiter RJ. Melatonin synthesis genes N-acetylserotonin methyltransferases evolved into caffeic acid O-methyltransferases and both assisted in plant terrestrialization. J Pineal Res 2021; 71:e12737. [PMID: 33844336 DOI: 10.1111/jpi.12737] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/25/2021] [Accepted: 04/07/2021] [Indexed: 11/28/2022]
Abstract
Terrestrialization is one of the most momentous events in the history of plant life, which leads to the subsequent evolution of plant diversity. The transition species, in this process, had to acquire a range of adaptive mechanisms to cope with the harsh features of terrestrial environments compared to that of aquatic habitat. As an ancient antioxidant, a leading regulator of ROS signaling or homeostasis, and a presumed plant master regulator, melatonin likely assisted plants transition to land and their adaption to terrestrial ecosystems. N-acetylserotonin methyltransferases (ASMT) and caffeic acid O-methyltransferases (COMT), both in the O-methyltransferase (OMT) family, catalyze the core O-methylation reaction in melatonin biosynthesis. How these two enzymes with close relevance evolved in plant evolutionary history and whether they participated in plant terrestrialization remains unknown. Using combined phylogenetic evidence and protein structure analysis, it is revealed that COMT likely evolved from ASMT by gene duplication and subsequent divergence. Newly emergent COMT gained a significantly higher ASMT activity to produce greater amounts of melatonin for immobile plants to acclimate to the stressful land environments after evolving from the more environmentally-stable aquatic conditions. The COMT genes possess more conserved substrate-binding sites at the amino acid level and more open protein conformation compared to ASMT, and getting a new function to catalyze the lignin biosynthesis. This development directly contributed to the dominance of vascular plants among the Earth's flora and prompted plant colonization of land. Thus, ASMT, together with its descendant COMT, might play key roles in plant transition to land. The current study provides new insights into plant terrestrialization with gene duplication contributing to this process along with well-known horizontal gene transfer.
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Affiliation(s)
- Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Zhengping Yao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
| | - Jiemei Zhang
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
| | - Renjun Zhang
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
| | - Zongmin Mou
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Xue Zhang
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
| | - Zonghang Li
- School of Life Science, Yunnan University, Kunming, China
| | - Xiaoli Feng
- School of Life Science, Yunnan University, Kunming, China
| | - Suiyun Chen
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health, Long School of Medicine, San Antonio, TX, USA
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13
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Furumizu C, Krabberød AK, Hammerstad M, Alling RM, Wildhagen M, Sawa S, Aalen RB. The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling. THE PLANT CELL 2021; 33:2915-2934. [PMID: 34240188 PMCID: PMC8462819 DOI: 10.1093/plcell/koab173] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in non-angiosperms. These discoveries provoke questions regarding co-evolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.
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Affiliation(s)
- Chihiro Furumizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Anders K Krabberød
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, Norway
| | - Renate M Alling
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Mari Wildhagen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Reidunn B Aalen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
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14
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Yao J, Scaffidi A, Meng Y, Melville KT, Komatsu A, Khosla A, Nelson DC, Kyozuka J, Flematti GR, Waters MT. Desmethyl butenolides are optimal ligands for karrikin receptor proteins. THE NEW PHYTOLOGIST 2021; 230:1003-1016. [PMID: 33474738 DOI: 10.1111/nph.17224] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/16/2021] [Indexed: 05/25/2023]
Abstract
Strigolactones and karrikins are butenolide molecules that regulate plant growth. They are perceived by the α/β-hydrolase DWARF14 (D14) and its homologue KARRIKIN INSENSITIVE2 (KAI2), respectively. Plant-derived strigolactones have a butenolide ring with a methyl group that is essential for bioactivity. By contrast, karrikins are abiotic in origin, and the butenolide methyl group is nonessential. KAI2 is probably a receptor for an endogenous butenolide, but the identity of this compound remains unknown. Here we characterise the specificity of KAI2 towards differing butenolide ligands using genetic and biochemical approaches. We find that KAI2 proteins from multiple species are most sensitive to desmethyl butenolides that lack a methyl group. Desmethyl-GR24 and desmethyl-CN-debranone are active by KAI2 but not D14. They are more potent KAI2 agonists compared with their methyl-substituted reference compounds both in vitro and in plants. The preference of KAI2 for desmethyl butenolides is conserved in Selaginella moellendorffii and Marchantia polymorpha, suggesting that it is an ancient trait in land plant evolution. Our findings provide insight into the mechanistic basis for differential ligand perception by KAI2 and D14, and support the view that the endogenous substrates for KAI2 and D14 have distinct chemical structures and biosynthetic origins.
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Affiliation(s)
- Jiaren Yao
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Adrian Scaffidi
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yongjie Meng
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Kim T Melville
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Aino Komatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Aashima Khosla
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Gavin R Flematti
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mark T Waters
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
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15
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Bellini E, Betti C, Sanità di Toppi L. Responses to Cadmium in Early-Diverging Streptophytes (Charophytes and Bryophytes): Current Views and Potential Applications. PLANTS (BASEL, SWITZERLAND) 2021; 10:770. [PMID: 33919852 PMCID: PMC8070800 DOI: 10.3390/plants10040770] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022]
Abstract
Several transition metals are essential for plant growth and development, as they are involved in various fundamental metabolic functions. By contrast, cadmium (Cd) is a metal that can prove extremely toxic for plants and other organisms in a dose-dependent manner. Charophytes and bryophytes are early-diverging streptophytes widely employed for biomonitoring purposes, as they are able to cope with high concentrations of toxic metal(loid)s without showing any apparent heavy damage. In this review, we will deal with different mechanisms that charophytes and bryophytes have evolved to respond to Cd at a cellular level. Particular attention will be addressed to strategies involving Cd vacuolar sequestration and cell wall immobilization, focusing on specific mechanisms that help achieve detoxification. Understanding the effects of metal(loid) pollution and accumulation on the morpho-physiological traits of charophytes and bryophytes can be in fact fundamental for optimizing their use as phytomonitors and/or phytoremediators.
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Affiliation(s)
- Erika Bellini
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (E.B.); (L.S.d.T.)
| | - Camilla Betti
- Department of Medicine, University of Perugia, 06132 Perugia, Italy
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16
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Ślipiko M, Myszczyński K, Buczkowska K, Bączkiewicz A, Szczecińska M, Sawicki J. Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes. BMC PLANT BIOLOGY 2020; 20:243. [PMID: 32466772 PMCID: PMC7257191 DOI: 10.1186/s12870-020-02435-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 05/10/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification. RESULTS On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%. CONCLUSIONS This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.
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Affiliation(s)
- Monika Ślipiko
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Buczkowska
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Alina Bączkiewicz
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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17
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Liang Z, Geng Y, Ji C, Du H, Wong CE, Zhang Q, Zhang Y, Zhang P, Riaz A, Chachar S, Ding Y, Wen J, Wu Y, Wang M, Zheng H, Wu Y, Demko V, Shen L, Han X, Zhang P, Gu X, Yu H. Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901850. [PMID: 31921561 PMCID: PMC6947507 DOI: 10.1002/advs.201901850] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/10/2019] [Indexed: 05/02/2023]
Abstract
The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
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Affiliation(s)
- Zhe Liang
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Yuke Geng
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Changmian Ji
- Biomarker TechnologiesBeijing101300China
- Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou571101China
| | - Hai Du
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Chui Eng Wong
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Qian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Ye Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Pingxian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Adeel Riaz
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Sadaruddin Chachar
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Yike Ding
- Department of EntomologyUniversity of California RiversideRiversideCA92521USA
| | - Jing Wen
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Yunwen Wu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | | | | | - Yanmin Wu
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Viktor Demko
- Department of Plant PhysiologyFaculty of Natural SciencesComenius University in BratislavaBratislava84215Slovakia
| | - Lisha Shen
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
| | - Xiao Han
- College of Biological Science and EngineeringFuzhou UniversityFuzhou350108China
| | - Pengpeng Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiaofeng Gu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Hao Yu
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
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18
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Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nat Commun 2019; 10:3480. [PMID: 31375675 PMCID: PMC6677796 DOI: 10.1038/s41467-019-11471-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/05/2019] [Indexed: 01/08/2023] Open
Abstract
An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips along with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land.
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Affiliation(s)
- Yuzhou Zhang
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, China
| | - Xiaojuan Wang
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, China
- College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Xixi Zhang
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
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19
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20
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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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21
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Bizotto FM, Ceratti RS, Braz AS, Masuda HP. Evolutionary history of Mo25 gene in plants, a component of RAM/MOR signaling network. Mech Dev 2018; 153:64-73. [DOI: 10.1016/j.mod.2018.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 07/05/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
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22
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Alcaraz LD, Peimbert M, Barajas HR, Dorantes-Acosta AE, Bowman JL, Arteaga-Vázquez MA. Marchantia liverworts as a proxy to plants' basal microbiomes. Sci Rep 2018; 8:12712. [PMID: 30140076 DOI: 10.1101/103861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/13/2018] [Indexed: 05/26/2023] Open
Abstract
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA genes of microbiomes two Marchantia species of liverworts. We compared microbiomes from M. polymorpha and M. paleacea plants collected in the wild relative to their soils substrates and from plants grown in vitro that were established from gemmae obtained from the same populations of wild plants. Our experimental setup allowed identification of microbes found in both native and in vitro Marchantia species. The main OTUs (97% identity) in Marchantia microbiomes were assigned to the following genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudate degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant. Based on their long evolutionary history Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational contribution of microbiomes to plant development and their response to environmental changes.
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Affiliation(s)
- Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, UNAM, 04510, Coyoacán, Mexico City, Mexico.
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, 05348, Mexico City, Mexico
| | - Hugo R Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, UNAM, 04510, Coyoacán, Mexico City, Mexico
| | - Ana E Dorantes-Acosta
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Mario A Arteaga-Vázquez
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico.
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23
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Fontanini D, Andreucci A, Ruffini Castiglione M, Basile A, Sorbo S, Petraglia A, Degola F, Bellini E, Bruno L, Varotto C, Sanità di Toppi L. The phytochelatin synthase from Nitella mucronata (Charophyta) plays a role in the homeostatic control of iron(II)/(III). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:88-96. [PMID: 29554573 DOI: 10.1016/j.plaphy.2018.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Although some charophytes (sister group to land plants) have been shown to synthesize phytochelatins (PCs) in response to cadmium (Cd), the functional characterization of their phytochelatin synthase (PCS) is still completely lacking. To investigate the metal response and the presence of PCS in charophytes, we focused on the species Nitella mucronata. A 40 kDa immunoreactive PCS band was revealed in mono-dimensional western blot by using a polyclonal antibody against Arabidopsis thaliana PCS1. In two-dimensional western blot, the putative PCS showed various spots with acidic isoelectric points, presumably originated by post-translational modifications. Given the PCS constitutive expression in N. mucronata, we tested its possible involvement in the homeostasis of metallic micronutrients, using physiological concentrations of iron (Fe) and zinc (Zn), and verified its role in the detoxification of a non-essential metal, such as Cd. Neither in vivo nor in vitro exposure to Zn resulted in PCS activation and PC significant biosynthesis, while Fe(II)/(III) and Cd were able to activate the PCS in vitro, as well as to induce PC accumulation in vivo. While Cd toxicity was evident from electron microscopy observations, the normal morphology of cells and organelles following Fe treatments was preserved. The overall results support a function of PCS and PCs in managing Fe homeostasis in the carophyte N. mucronata.
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Affiliation(s)
| | | | | | - Adriana Basile
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Sergio Sorbo
- CeSMA, Microscopy Section, University of Naples "Federico II", Naples, Italy
| | - Alessandro Petraglia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Degola
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Erika Bellini
- Department of Biology, University of Pisa, Pisa, Italy; Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Laura Bruno
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, "Edmund Mach" Foundation, S. Michele all'Adige (TN), Italy
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24
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Kenrick P. Changing expressions: a hypothesis for the origin of the vascular plant life cycle. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170149. [PMID: 29254970 PMCID: PMC5745341 DOI: 10.1098/rstb.2017.0149] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 02/06/2023] Open
Abstract
Plant life cycles underwent fundamental changes during the initial colonization of the land in the Early Palaeozoic, shaping the direction of evolution. Fossils reveal unanticipated diversity, including new variants of meiotic cell division and leafless gametophytes with mycorrhizal-like symbioses, rhizoids, vascular tissues and stomata. Exceptional fossils from the 407-Ma Rhynie chert (Scotland) play a key role in unlocking this diversity. These fossils are reviewed against progress in our understanding of the plant tree of life and recent advances in developmental genetics. Combining data from different sources sheds light on a switch in life cycle that gave rise to the vascular plants. One crucial step was the establishment of a free-living sporophyte from one that was an obligate matrotroph borne on the gametophyte. It is proposed that this difficult evolutionary transition was achieved through expansion of gene expression primarily from the gametophyte to the sporophyte, establishing a now extinct life cycle variant that was more isomorphic than heteromorphic. These changes also linked for the first time in one developmental system rhizoids, vascular tissues and stomata, putting in place the critical components that regulate transpiration and forming a physiological platform of primary importance to the diversification of vascular plants.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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25
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Renault H, De Marothy M, Jonasson G, Lara P, Nelson DR, Nilsson I, André F, von Heijne G, Werck-Reichhart D. Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants. Mol Biol Evol 2018; 34:2041-2056. [PMID: 28505373 PMCID: PMC5850782 DOI: 10.1093/molbev/msx160] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Evolution of the phenolic metabolism was critical for the transition of plants from water to land. A cytochrome P450, CYP73, with cinnamate 4-hydroxylase (C4H) activity, catalyzes the first plant-specific and rate-limiting step in this pathway. The CYP73 gene is absent from green algae, and first detected in bryophytes. A CYP73 duplication occurred in the ancestor of seed plants and was retained in Taxaceae and most angiosperms. In spite of a clear divergence in primary sequence, both paralogs can fulfill comparable cinnamate hydroxylase roles both in vitro and in vivo. One of them seems dedicated to the biosynthesis of lignin precursors. Its N-terminus forms a single membrane spanning helix and its properties and length are highly constrained. The second is characterized by an elongated and variable N-terminus, reminiscent of ancestral CYP73s. Using as proxies the Brachypodium distachyon proteins, we show that the elongation of the N-terminus does not result in an altered subcellular localization, but in a distinct membrane topology. Insertion in the membrane of endoplasmic reticulum via a double-spanning open hairpin structure allows reorientation to the lumen of the catalytic domain of the protein. In agreement with participation to a different functional unit and supramolecular organization, the protein displays modified heme proximal surface. These data suggest the evolution of divergent C4H enzymes feeding different branches of the phenolic network in seed plants. It shows that specialization required for retention of gene duplicates may result from altered protein topology rather than change in enzyme activity.
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Affiliation(s)
- Hugues Renault
- Centre National de la Recherche Scientifique, Institute of Plant Molecular Biology, University of Strasbourg, Strasbourg, France
| | - Minttu De Marothy
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Gabriella Jonasson
- Institute for Integrative Biology of the Cell (I2BC), DRF/Joliot/SB2SM, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Patricia Lara
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - François André
- Institute for Integrative Biology of the Cell (I2BC), DRF/Joliot/SB2SM, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Danièle Werck-Reichhart
- Centre National de la Recherche Scientifique, Institute of Plant Molecular Biology, University of Strasbourg, Strasbourg, France
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26
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Schmid MW, Giraldo-Fonseca A, Rövekamp M, Smetanin D, Bowman JL, Grossniklaus U. Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha. Genome Biol 2018; 19:9. [PMID: 29368664 PMCID: PMC5784723 DOI: 10.1186/s13059-017-1383-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/21/2017] [Indexed: 12/19/2022] Open
Abstract
Background In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles. Results Of all cytosines tested for differential DNA methylation, 42% vary significantly in their methylation pattern throughout the life cycle. However, the differences are limited to few comparisons between specific stages of the life cycle and suggest four major epigenetic states specific to sporophytes, vegetative gametophytes, antherozoids, and archegonia. Further analyses indicated clear differences in the mechanisms underlying reprogramming in the gametophytic and sporophytic generations, which are paralleled by differences in the expression of genes involved in DNA methylation. Differentially methylated cytosines with a gain in methylation in antherozoids and archegonia are enriched in the CG and CHG contexts, as well as in gene bodies and gene flanking regions. In contrast, gain of DNA methylation during sporophyte development is mostly limited to the CHH context, LTR retrotransposons, DNA transposons, and repeats. Conclusion We conclude that epigenetic reprogramming occurs at least twice during the life cycle of M. polymorpha and that the underlying mechanisms are likely different between the two events. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1383-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc W Schmid
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - John L Bowman
- Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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27
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Kato H, Nishihama R, Weijers D, Kohchi T. Evolution of nuclear auxin signaling: lessons from genetic studies with basal land plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:291-301. [PMID: 28992186 DOI: 10.1093/jxb/erx267] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Auxin plays critical roles in growth and development through the regulation of cell differentiation, cell expansion, and pattern formation. The auxin signal is mainly conveyed through a so-called nuclear auxin pathway involving the receptor TIR1/AFB, the transcriptional co-repressor AUX/IAA, and the transcription factor ARF with direct DNA-binding ability. Recent progress in sequence information and molecular genetics in basal plants has provided many insights into the evolutionary origin of the nuclear auxin pathway and its pleiotropic roles in land plant development. In this review, we summarize the latest knowledge of the nuclear auxin pathway gained from studies using basal plants, including charophycean green algae and two major model bryophytes, Marchantia polymorpha and Physcomitrella patens. In addition, we discuss the functional implication of the increase in genetic complexity of the nuclear auxin pathway during land plant evolution.
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Affiliation(s)
- Hirotaka Kato
- Laboratory of Biochemistry, Wageningen University, The Netherlands
| | | | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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28
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Hansen LL, Nielsen ME. Plant exosomes: using an unconventional exit to prevent pathogen entry? JOURNAL OF EXPERIMENTAL BOTANY 2017; 69:59-68. [PMID: 29036447 DOI: 10.1093/jxb/erx319] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ability to ward off filamentous pathogens, such as powdery mildew fungi, is one of the best studied examples of membrane trafficking-dependent disease resistance in plants. Here, papilla formation at the site of attack is essential for the pre-invasive immunity, whereas the encasement can hamper disease post-invasively. Exosomes containing antifungal peptides and small RNAs are thought to play a vital role in forming papillae and encasements that block fungal growth. While exosomes are well described in mammals, and have been shown to play important roles in cell-cell communication regulating development and disease, their function is not well-known in plants. In this review, we focus on some of the recent discoveries on plant exosomes and try to link this information with our current understanding of how plants use this form of unconventional secretion to acquire this durable and effective form of resistance.
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Affiliation(s)
- Line Lykke Hansen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center (CPSC), University of Copenhagen, Denmark
| | - Mads Eggert Nielsen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center (CPSC), University of Copenhagen, Denmark
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29
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Linde A, Eklund DM, Kubota A, Pederson ERA, Holm K, Gyllenstrand N, Nishihama R, Cronberg N, Muranaka T, Oyama T, Kohchi T, Lagercrantz U. Early evolution of the land plant circadian clock. THE NEW PHYTOLOGIST 2017; 216:576-590. [PMID: 28244104 PMCID: PMC5638080 DOI: 10.1111/nph.14487] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.
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Affiliation(s)
- Anna‐Malin Linde
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - D. Magnus Eklund
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Akane Kubota
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Eric R. A. Pederson
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Karl Holm
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Niclas Gyllenstrand
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | | | - Nils Cronberg
- Department of BiologyLund UniversityEcology BuildingSE‐22362LundSweden
| | | | - Tokitaka Oyama
- Graduate School of ScienceKyoto UniversityKyoto606‐8502Japan
| | - Takayuki Kohchi
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
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30
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Abstract
Strigolactones are a structurally diverse class of plant hormones that control many aspects of shoot and root growth. Strigolactones are also exuded by plants into the rhizosphere, where they promote symbiotic interactions with arbuscular mycorrhizal fungi and germination of root parasitic plants in the Orobanchaceae family. Therefore, understanding how strigolactones are made, transported, and perceived may lead to agricultural innovations as well as a deeper knowledge of how plants function. Substantial progress has been made in these areas over the past decade. In this review, we focus on the molecular mechanisms, core developmental roles, and evolutionary history of strigolactone signaling. We also propose potential translational applications of strigolactone research to agriculture.
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Affiliation(s)
- Mark T Waters
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth 6009, Australia;
| | - Caroline Gutjahr
- Genetics, Faculty of Biology, LMU Munich, 82152 Martinsried, Germany;
| | - Tom Bennett
- School of Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521;
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31
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Renault H, Alber A, Horst NA, Basilio Lopes A, Fich EA, Kriegshauser L, Wiedemann G, Ullmann P, Herrgott L, Erhardt M, Pineau E, Ehlting J, Schmitt M, Rose JKC, Reski R, Werck-Reichhart D. A phenol-enriched cuticle is ancestral to lignin evolution in land plants. Nat Commun 2017; 8:14713. [PMID: 28270693 PMCID: PMC5344971 DOI: 10.1038/ncomms14713] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/24/2017] [Indexed: 12/22/2022] Open
Abstract
Lignin, one of the most abundant biopolymers on Earth, derives from the plant phenolic metabolism. It appeared upon terrestrialization and is thought critical for plant colonization of land. Early diverging land plants do not form lignin, but already have elements of its biosynthetic machinery. Here we delete in a moss the P450 oxygenase that defines the entry point in angiosperm lignin metabolism, and find that its pre-lignin pathway is essential for development. This pathway does not involve biochemical regulation via shikimate coupling, but instead is coupled with ascorbate catabolism, and controls the synthesis of the moss cuticle, which prevents desiccation and organ fusion. These cuticles share common features with lignin, cutin and suberin, and may represent the extant representative of a common ancestor. Our results demonstrate a critical role for the ancestral phenolic metabolism in moss erect growth and cuticle permeability, consistent with importance in plant adaptation to terrestrial conditions. The phenolic polymer lignin is thought to have contributed to adaptation of early land plants to terrestrial environments. Here Renault et al. show that moss, which does not produce lignin, contains an ancestral phenolic metabolism pathway that produces a phenol-enriched cuticle and prevents desiccation.
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Affiliation(s)
- Hugues Renault
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France.,Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany.,University of Strasbourg Institute for Advanced Study, 5 allée du Général Rouvillois, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
| | - Annette Alber
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France.,Department of Biology &Centre for Forest Biology, University of Victoria, British Columbia, Canada V8P 5C2
| | - Nelly A Horst
- Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Alexandra Basilio Lopes
- Laboratoire d'Innovation Thérapeutique, UMR CNRS 7200, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Eric A Fich
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Lucie Kriegshauser
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Gertrud Wiedemann
- Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Pascaline Ullmann
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Laurence Herrgott
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Mathieu Erhardt
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Emmanuelle Pineau
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Jürgen Ehlting
- Department of Biology &Centre for Forest Biology, University of Victoria, British Columbia, Canada V8P 5C2
| | - Martine Schmitt
- Laboratoire d'Innovation Thérapeutique, UMR CNRS 7200, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Ralf Reski
- Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany.,University of Strasbourg Institute for Advanced Study, 5 allée du Général Rouvillois, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Danièle Werck-Reichhart
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France.,University of Strasbourg Institute for Advanced Study, 5 allée du Général Rouvillois, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
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32
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Han GZ. Evolution of jasmonate biosynthesis and signaling mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1323-1331. [PMID: 28007954 DOI: 10.1093/jxb/erw470] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Jasmonates are phytohormones that modulate a wide spectrum of plant physiological processes, especially defense against herbivores and necrotrophs. The molecular mechanisms of jasmonate biosynthesis and signaling have been well characterized in model plants. In this review, we provide an in-depth analysis and overview of the origin and evolution of the jasmonate biosynthesis and signaling pathways. Furthermore, we discuss the striking parallels between jasmonate and auxin signaling mechanisms, which reveals a common ancestry of these signaling mechanisms. Finally, we highlight the importance of studying jasmonate biosynthesis and signaling in lower plants.
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Affiliation(s)
- Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210046, China
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33
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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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34
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Brunkard JO, Zambryski PC. Plasmodesmata enable multicellularity: new insights into their evolution, biogenesis, and functions in development and immunity. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:76-83. [PMID: 27889635 DOI: 10.1016/j.pbi.2016.11.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 05/19/2023]
Abstract
Plant cells are connected by plasmodesmata (PD), cytosolic bridges that allow molecules to freely move across the cell wall. Recently resolved relationships among land plants and their algal relatives reveal that land plants evolved PD independently from algae. Proteomic and genetic screens illuminate new dimensions of the structural and regulatory pathways that control PD biogenesis. Biochemical studies demonstrate that immunological signals induce systemic defenses by moving from diseased cells through PD; subsequently, PD transport is restricted to quarantine diseased cells. Here, we review our expanding knowledge of the roles of PD in plant development, physiology, and immunity.
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Affiliation(s)
- Jacob O Brunkard
- Plant Gene Expression Center, USDA Agricultural Research Service, 800 Buchanan Street, Albany, CA 94710, USA
| | - Patricia C Zambryski
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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35
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Ishizaki K. Evolution of land plants: insights from molecular studies on basal lineages. Biosci Biotechnol Biochem 2017; 81:73-80. [DOI: 10.1080/09168451.2016.1224641] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.
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Affiliation(s)
- Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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36
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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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37
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Shchennikova AV, Beletsky AV, Shulga OA, Mazur AM, Prokhortchouk EB, Kochieva EZ, Ravin NV, Skryabin KG. Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys. PLANT MOLECULAR BIOLOGY 2016; 91:441-458. [PMID: 27097902 DOI: 10.1007/s11103-016-0478-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Myco-heterotroph Monotropa hypopitys is a widely spread perennial herb used to study symbiotic interactions and physiological mechanisms underlying the development of non-photosynthetic plant. Here, we performed, for the first time, transcriptome-wide characterization of M. hypopitys miRNA profile using high throughput Illumina sequencing. As a result of small RNA library sequencing and bioinformatic analysis, we identified 55 members belonging to 40 families of known miRNAs and 17 putative novel miRNAs unique for M. hypopitys. Computational screening revealed 206 potential mRNA targets for known miRNAs and 31 potential mRNA targets for novel miRNAs. The predicted target genes were described in Gene Ontology terms and were found to be involved in a broad range of metabolic and regulatory pathways. The identification of novel M. hypopitys-specific miRNAs, some with few target genes and low abundances, suggests their recent evolutionary origin and participation in highly specialized regulatory mechanisms fundamental for non-photosynthetic biology of M. hypopitys. This global analysis of miRNAs and their potential targets in M. hypopitys provides a framework for further investigation of miRNA role in the evolution and establishment of non-photosynthetic myco-heterotrophs.
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Affiliation(s)
- Anna V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Olga A Shulga
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexander M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Egor B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Elena Z Kochieva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Nikolay V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Konstantin G Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071.
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38
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Rövekamp M, Bowman JL, Grossniklaus U. Marchantia MpRKD Regulates the Gametophyte-Sporophyte Transition by Keeping Egg Cells Quiescent in the Absence of Fertilization. Curr Biol 2016; 26:1782-1789. [PMID: 27345166 DOI: 10.1016/j.cub.2016.05.028] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 12/21/2022]
Abstract
Unlike in animals, the life cycle of land plants alternates between two multicellular generations, the haploid gametophyte and the diploid sporophyte [1]. Gamete differentiation initiates the transition from the gametophyte to the sporophyte generation and, upon maturation, the egg cell establishes a quiescent state that is maintained until fertilization. This quiescence represents a hallmark of the gametophyte-sporophyte transition. The underlying molecular mechanisms are complex and best characterized in the flowering plant Arabidopsis thaliana [2-4]. However, only few genes with egg cell-specific expression or defects have been identified [5-10]. Intriguingly, ectopic expression of members of a clade of RWP-RK domain (RKD)-containing transcription factors, which are absent from animal genomes [11-13], can induce an egg cell-like transcriptome in sporophytic cells of A. thaliana. Yet, to date, loss-of-function experiments have not produced phenotypes affecting the egg cell, likely due to genetic redundancy and/or cross-regulation among the five RKD genes of A. thaliana [10]. To reduce genetic complexity, we explored the genome of Marchantia polymorpha, a liverwort belonging to the basal lineage of extant land plants [14-17]. Based on sequence homology, we identified a single M. polymorpha RKD gene, MpRKD, which is orthologous to all five A. thaliana RKD genes. Analysis of the MpRKD expression pattern and characterization of lines with reduced MpRKD activity indicate that it functions as a regulator of gametophyte development and the gametophyte-sporophyte transition. In particular, MpRKD is required to establish and/or maintain the quiescent state of the egg cell in the absence of fertilization.
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Affiliation(s)
- Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia; Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland.
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Breuninger H, Thamm A, Streubel S, Sakayama H, Nishiyama T, Dolan L. Diversification of a Transcription Factor Family Led to the Evolution of Antagonistically Acting Genetic Regulators of Root Hair Growth. Curr Biol 2016; 26:1622-1628. [PMID: 27265398 PMCID: PMC4920954 DOI: 10.1016/j.cub.2016.04.060] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/11/2016] [Accepted: 04/25/2016] [Indexed: 10/25/2022]
Abstract
Streptophytes colonized the land some time before 470 million years ago [1-3]. The colonization coincided with an increase in morphological and cellular diversity [4-7]. This increase in diversity is correlated with a proliferation in transcription factors encoded in genomes [8-10]. This suggests that gene duplication and subsequent diversification of function was instrumental in the generation of land plant diversity. Here, we investigate the diversification of the streptophyte-specific Lotus japonicus ROOTHAIRLESS LIKE (LRL) transcription factor (TF) [11, 12] subfamily of basic loop helix (bHLH) proteins by comparing gene function in early divergent and derived land plant species. We report that the single Marchantia polymorpha LRL gene acts as a general growth regulator required for rhizoid development, a function that has been partially conserved throughout multicellular streptophytes. In contrast, the five relatively derived Arabidopsis thaliana LRL genes comprise two antagonistically acting groups of differentially expressed genes. The diversification of LRL genes accompanied the evolution of an antagonistic regulatory element controlling root hair development.
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Affiliation(s)
- Holger Breuninger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Anna Thamm
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Susanna Streubel
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Hidetoshi Sakayama
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa 920-0934, Japan
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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40
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Lin PC, Lu CW, Shen BN, Lee GZ, Bowman JL, Arteaga-Vazquez MA, Liu LYD, Hong SF, Lo CF, Su GM, Kohchi T, Ishizaki K, Zachgo S, Althoff F, Takenaka M, Yamato KT, Lin SS. Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses. PLANT & CELL PHYSIOLOGY 2016; 57:339-58. [PMID: 26861787 PMCID: PMC4788410 DOI: 10.1093/pcp/pcw020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 11/22/2015] [Indexed: 05/04/2023]
Abstract
Bryophytes (liverworts, hornworts and mosses) comprise the three earliest diverging lineages of land plants (embryophytes). Marchantia polymorpha, a complex thalloid Marchantiopsida liverwort that has been developed into a model genetic system, occupies a key phylogenetic position. Therefore, M. polymorpha is useful in studies aiming to elucidate the evolution of gene regulation mechanisms in plants. In this study, we used computational, transcriptomic, small RNA and degradome analyses to characterize microRNA (miRNA)-mediated pathways of gene regulation in M. polymorpha. The data have been integrated into the open access ContigViews-miRNA platform for further reference. In addition to core components of the miRNA pathway, 129 unique miRNA sequences, 11 of which could be classified into seven miRNA families that are conserved in embryophytes (miR166a, miR390, miR529c, miR171-3p, miR408a, miR160 and miR319a), were identified. A combination of computational and degradome analyses allowed us to identify and experimentally validate 249 targets. In some cases, the target genes are orthologous to those of other embryophytes, but in other cases, the conserved miRNAs target either paralogs or members of different gene families. In addition, the newly discovered Mpo-miR11707.1 and Mpo-miR11707.2 are generated from a common precursor and target MpARGONAUTE1 (LW1759). Two other newly discovered miRNAs, Mpo-miR11687.1 and Mpo-miR11681.1, target the MADS-box transcription factors MpMADS1 and MpMADS2, respectively. Interestingly, one of the pentatricopeptide repeat (PPR) gene family members, MpPPR_66 (LW9825), the protein products of which are generally involved in various steps of RNA metabolism, has a long stem-loop transcript that can generate Mpo-miR11692.1 to autoregulate MpPPR_66 (LW9825) mRNA. This study provides a foundation for further investigations of the RNA-mediated silencing mechanism in M. polymorpha as well as of the evolution of this gene silencing pathway in embryophytes.
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Affiliation(s)
- Pin-Chun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106 These authors contributed equally to this work
| | - Chia-Wei Lu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106 These authors contributed equally to this work
| | - Bing-Nan Shen
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106
| | - Guan-Zong Lee
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Mario A Arteaga-Vazquez
- Instituto de Biotecnologia y Ecologia Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa Veracruz, Mexico
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University, 1 Sec. 4, Roosevelt Rd. Taipei, Taiwan 106
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106
| | - Chu-Fang Lo
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Taiwan 701
| | - Gong-Min Su
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | | | - Sabine Zachgo
- University of Osnabrück, Botany Department, D-49076 Osnabrück, Germany
| | - Felix Althoff
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106
| | - Mizuki Takenaka
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Nishimitani, Kinokawa, Wakayama, 649-6493 Japan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106 Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 115 Center of Biotechnology, National Taiwan University, Taipei, Taiwan 106
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41
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Horst NA, Katz A, Pereman I, Decker EL, Ohad N, Reski R. A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction. NATURE PLANTS 2016; 2:15209. [PMID: 27250874 DOI: 10.1038/nplants.2015.209] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/27/2015] [Indexed: 05/17/2023]
Abstract
Plants characteristically alternate between haploid gametophytic and diploid sporophytic stages. Meiosis and fertilization respectively initiate these two different ontogenies(1). Genes triggering ectopic embryo development on vegetative sporophytic tissues are well described(2,3); however, a genetic control of embryo development from gametophytic tissues remains elusive. Here, in the moss Physcomitrella patens we show that ectopic overexpression of the homeobox gene BELL1 induces embryo formation and subsequently reproductive diploid sporophytes from specific gametophytic cells without fertilization. In line with this, BELL1 loss-of-function mutants have a wild-type phenotype, except that their egg cells are bigger and unable to form embryos. Our results identify BELL1 as a master regulator for the gametophyte-to-sporophyte transition in P. patens and provide mechanistic insights into the evolution of embryos that can generate multicellular diploid sporophytes. This developmental innovation facilitated the colonization of land by plants about 500 million years ago(4) and thus shaped our current ecosystems.
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Affiliation(s)
- Nelly A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Aviva Katz
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Idan Pereman
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Nir Ohad
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 69978, Israel
- The Manna Center Program for Food Safety &Security, Tel Aviv University, Tel-Aviv 69978, Israel
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
- FRIAS - Freiburg Institute for Advanced Studies, 79104 Freiburg, Germany
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42
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Abstract
The genetic and molecular basis of the developmental programs underlying adaptive morphological changes is largely unknown. A new study reveals an ancient gene that has been instrumental for the generation of morphological diversity and adaptation in land plants.
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Affiliation(s)
- Mario A Arteaga-Vazquez
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, Xalapa, Veracruz, México.
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43
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Kawashima T, Lorković ZJ, Nishihama R, Ishizaki K, Axelsson E, Yelagandula R, Kohchi T, Berger F. Diversification of histone H2A variants during plant evolution. TRENDS IN PLANT SCIENCE 2015; 20:419-25. [PMID: 25983206 DOI: 10.1016/j.tplants.2015.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 05/19/2023]
Abstract
Among eukaryotes, the four core histones show an extremely high conservation of their structure and form nucleosomes that compact, protect, and regulate access to genetic information. Nevertheless, in multicellular eukaryotes the two families, histone H2A and histone H3, have diversified significantly in key residues. We present a phylogenetic analysis across the green plant lineage that reveals an early diversification of the H2A family in unicellular green algae and remarkable expansions of H2A variants in flowering plants. We define motifs and domains that differentiate plant H2A proteins into distinct variant classes. In non-flowering land plants, we identify a new class of H2A variants and propose their possible role in the emergence of the H2A.W variant class in flowering plants.
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Affiliation(s)
- Tomokazu Kawashima
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Frederic Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria.
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44
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Kato H, Ishizaki K, Kouno M, Shirakawa M, Bowman JL, Nishihama R, Kohchi T. Auxin-Mediated Transcriptional System with a Minimal Set of Components Is Critical for Morphogenesis through the Life Cycle in Marchantia polymorpha. PLoS Genet 2015; 11:e1005084. [PMID: 26020919 PMCID: PMC4447296 DOI: 10.1371/journal.pgen.1005084] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/20/2015] [Indexed: 01/06/2023] Open
Abstract
The plant hormone auxin regulates many aspects of plant growth and development. Recent progress in Arabidopsis provided a scheme that auxin receptors, TIR1/AFBs, target transcriptional co-repressors, AUX/IAAs, for degradation, allowing ARFs to regulate transcription of auxin responsive genes. The mechanism of auxin-mediated transcriptional regulation is considered to have evolved around the time plants adapted to land. However, little is known about the role of auxin-mediated transcription in basal land plant lineages. We focused on the liverwort Marchantia polymorpha, which belongs to the earliest diverging lineage of land plants. M. polymorpha has only a single TIR1/AFB (MpTIR1), a single AUX/IAA (MpIAA), and three ARFs (MpARF1, MpARF2, and MpARF3) in the genome. Expression of a dominant allele of MpIAA with mutations in its putative degron sequence conferred an auxin resistant phenotype and repressed auxin-dependent expression of the auxin response reporter proGH3:GUS. We next established a system for DEX-inducible auxin-response repression by expressing the putatively stabilized MpIAA protein fused with the glucocorticoid receptor domain (MpIAA(mDII)-GR). Repression of auxin responses in (pro)MpIAA:MpIAA(mDII)-GR plants caused severe defects in various developmental processes, including gemmaling development, dorsiventrality, organogenesis, and tropic responses. Transient transactivation assays showed that the three MpARFs had different transcriptional activities, each corresponding to their phylogenetic classifications. Moreover, MpIAA and MpARF proteins interacted with each other with different affinities. This study provides evidence that pleiotropic auxin responses can be achieved by a minimal set of auxin signaling factors and suggests that the transcriptional regulation mediated by TIR1/AFB, AUX/IAA, and three types of ARFs might have been a key invention to establish body plans of land plants. We propose that M. polymorpha is a good model to investigate the principles and the evolution of auxin-mediated transcriptional regulation and its roles in land plant morphogenesis.
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Affiliation(s)
- Hirotaka Kato
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Masaru Kouno
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Section of Plant Biology, University of California, Davis, Davis, California, United States of America
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- * E-mail:
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45
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Auxin-Mediated Transcriptional System with a Minimal Set of Components Is Critical for Morphogenesis through the Life Cycle in Marchantia polymorpha. PLoS Genet 2015. [DOI: 10.1371/journal.pgen.1005084 pgenetics-d-14-02665 [pii]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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46
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Flores-Sandoval E, Eklund DM, Bowman JL. A Simple Auxin Transcriptional Response System Regulates Multiple Morphogenetic Processes in the Liverwort Marchantia polymorpha. PLoS Genet 2015; 11:e1005207. [PMID: 26020649 PMCID: PMC4447368 DOI: 10.1371/journal.pgen.1005207] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/13/2015] [Indexed: 02/06/2023] Open
Abstract
In land plants comparative genomics has revealed that members of basal lineages share a common set of transcription factors with the derived flowering plants, despite sharing few homologous structures. The plant hormone auxin has been implicated in many facets of development in both basal and derived lineages of land plants. We functionally characterized the auxin transcriptional response machinery in the liverwort Marchantia polymorpha, a member of the basal lineage of extant land plants. All components known from flowering plant systems are present in M. polymorpha, but they exist as single orthologs: a single MpTOPLESS (TPL) corepressor, a single MpTRANSPORT inhibitor response 1 auxin receptor, single orthologs of each class of auxin response factor (ARF; MpARF1, MpARF2, MpARF3), and a single negative regulator auxin/indole-3-acetic acid (MpIAA). Phylogenetic analyses suggest this simple system is the ancestral condition for land plants. We experimentally demonstrate that these genes act in an auxin response pathway--chimeric fusions of the MpTPL corepressor with heterodimerization domains of MpARF1, MpARF2, or their negative regulator, MpIAA, generate auxin insensitive plants that lack the capacity to pattern and transition into mature stages of development. Our results indicate auxin mediated transcriptional regulation acts as a facilitator of branching, differentiation and growth, rather than acting to determine or specify tissues during the haploid stage of the M. polymorpha life cycle. We hypothesize that the ancestral role of auxin is to modulate a balance of differentiated and pluri- or totipotent cell states, whose fates are determined by interactions with combinations of unrelated transcription factors.
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Affiliation(s)
| | - D. Magnus Eklund
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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47
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Edwards D, Kenrick P. The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) 'On the plant-remains from the Downtonian of England and Wales'. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140343. [PMID: 25750238 PMCID: PMC4360123 DOI: 10.1098/rstb.2014.0343] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the 1920s, the botanist W. H. Lang set out to collect and investigate some very unpromising fossils of uncertain affinity, which predated the known geological record of life on land. His discoveries led to a landmark publication in 1937, 'On the plant-remains from the Downtonian of England and Wales', in which he revealed a diversity of small fossil organisms of great simplicity that shed light on the nature of the earliest known land plants. These and subsequent discoveries have taken on new relevance as botanists seek to understand the plant genome and the early evolution of fundamental organ systems. Also, our developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to our understanding of how life on land affects key Earth Systems (e.g. carbon cycle). The emerging paradigm is one of early life on land dominated by microbes, small bryophyte-like organisms and lichens. Collectively called cryptogamic covers, these are comparable with those that dominate certain ecosystems today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
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Affiliation(s)
- Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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48
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The cytosol must flow: intercellular transport through plasmodesmata. Curr Opin Cell Biol 2015; 35:13-20. [PMID: 25847870 DOI: 10.1016/j.ceb.2015.03.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/20/2015] [Accepted: 03/21/2015] [Indexed: 01/20/2023]
Abstract
Plant cells are connected across cell walls by nanoscopic channels called plasmodesmata (PD), which allow plant cells to share resources and exchange signaling molecules. Several protein components of PD membranes have been identified, and recent advances in superresolution live-cell microscopy are illuminating PD ultrastructure. Restricting transport through PD is crucial for morphogenesis, since hormones and hundreds of transcription factors regularly move through PD, and this transport must stop to allow cells to begin differentiating. Chloroplasts and mitochondria regulate PD function through signal transduction networks that coordinate plant physiology and development. Recent discoveries on the relationships of land plants and their algal relatives suggest that PD have evolved independently in several lineages, emphasizing the importance of cytosolic bridges in multicellular biology.
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49
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Alaba S, Piszczalka P, Pietrykowska H, Pacak AM, Sierocka I, Nuc PW, Singh K, Plewka P, Sulkowska A, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. THE NEW PHYTOLOGIST 2015; 206:352-367. [PMID: 25530158 PMCID: PMC4368373 DOI: 10.1111/nph.13220] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/10/2014] [Indexed: 05/03/2023]
Abstract
Liverworts are the most basal group of extant land plants. Nonetheless, the molecular biology of liverworts is poorly understood. Gene expression has been studied in only one species, Marchantia polymorpha. In particular, no microRNA (miRNA) sequences from liverworts have been reported. Here, Illumina-based next-generation sequencing was employed to identify small RNAs, and analyze the transcriptome and the degradome of Pellia endiviifolia. Three hundred and eleven conserved miRNA plant families were identified, and 42 new liverwort-specific miRNAs were discovered. The RNA degradome analysis revealed that target mRNAs of only three miRNAs (miR160, miR166, and miR408) have been conserved between liverworts and other land plants. New targets were identified for the remaining conserved miRNAs. Moreover, the analysis of the degradome permitted the identification of targets for 13 novel liverwort-specific miRNAs. Interestingly, three of the liverwort microRNAs show high similarity to previously reported miRNAs from Chlamydomonas reinhardtii. This is the first observation of miRNAs that exist both in a representative alga and in the liverwort P. endiviifolia but are not present in land plants. The results of the analysis of the P. endivifolia microtranscriptome support the conclusions of previous studies that placed liverworts at the root of the land plant evolutionary tree of life.
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Affiliation(s)
- Sylwia Alaba
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Pawel Piszczalka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Andrzej M Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Przemyslaw W Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Kashmir Singh
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Aleksandra Sulkowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Wojciech M Karlowski
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
| | - Zofia Szweykowska-Kulinska
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61-614, Poznań, Poland
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50
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Wang C, Liu Y, Li SS, Han GZ. Insights into the origin and evolution of the plant hormone signaling machinery. PLANT PHYSIOLOGY 2015; 167:872-86. [PMID: 25560880 PMCID: PMC4348752 DOI: 10.1104/pp.114.247403] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plant hormones modulate plant growth, development, and defense. However, many aspects of the origin and evolution of plant hormone signaling pathways remain obscure. Here, we use a comparative genomic and phylogenetic approach to investigate the origin and evolution of nine major plant hormone (abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonate, salicylic acid, and strigolactone) signaling pathways. Our multispecies genome-wide analysis reveals that: (1) auxin, cytokinin, and strigolactone signaling pathways originated in charophyte lineages; (2) abscisic acid, jasmonate, and salicylic acid signaling pathways arose in the last common ancestor of land plants; (3) gibberellin signaling evolved after the divergence of bryophytes from land plants; (4) the canonical brassinosteroid signaling originated before the emergence of angiosperms but likely after the split of gymnosperms and angiosperms; and (5) the origin of the canonical ethylene signaling pathway postdates shortly the emergence of angiosperms. Our findings might have important implications in understanding the molecular mechanisms underlying the emergence of land plants.
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Affiliation(s)
- Chunyang Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China (C.W., G.-Z.H.);State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China (C.W., Y.L., S.-S.L.); andDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 (G.-Z.H.)
| | - Yang Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China (C.W., G.-Z.H.);State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China (C.W., Y.L., S.-S.L.); andDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 (G.-Z.H.)
| | - Si-Shen Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China (C.W., G.-Z.H.);State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China (C.W., Y.L., S.-S.L.); andDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 (G.-Z.H.)
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China (C.W., G.-Z.H.);State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China (C.W., Y.L., S.-S.L.); andDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 (G.-Z.H.)
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