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Kimura I, Kanegae T. A phytochrome/phototropin chimeric photoreceptor promotes growth of fern gametophytes under limited light conditions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2403-2416. [PMID: 38189579 DOI: 10.1093/jxb/erae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/06/2024] [Indexed: 01/09/2024]
Abstract
Many ferns thrive even in low-light niches such as under an angiosperm forest canopy. However, the shade adaptation strategy of ferns is not well understood. Phytochrome 3/neochrome (phy3/neo) is an unconventional photoreceptor, found in the fern Adiantum capillus-veneris, that controls both red and blue light-dependent phototropism and chloroplast photorelocation, which are considered to improve photosynthetic efficiency in ferns. Here we show that phy3/neo localizes not only at the plasma membrane but also in the nucleus. Since both phototropism and chloroplast photorelocation are mediated by membrane-associated phototropin photoreceptors, we speculated that nucleus-localized phy3/neo possesses a previously undescribed biological function. We reveal that phy3/neo directly interacts with Adiantum cryptochrome 3 (cry3) in the nucleus. Plant cryptochromes are blue light receptors that transcriptionally regulate photomorphogenesis; therefore, phy3/neo may function via cry3 to synchronize light-mediated development with phototropism and chloroplast photorelocation to promote fern growth under low-light conditions. Furthermore, we demonstrate that phy3/neo regulates the expression of the Cyclin-like gene AcCyc1 and promotes prothallium expansion growth. These findings provide insight into the shade adaptation strategy of ferns and suggest that phy3/neo plays a substantial role in the survival and growth of ferns during the tiny gametophytic stage under low-light conditions, such as those on the forest floor.
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Affiliation(s)
- Izumi Kimura
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Takeshi Kanegae
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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Sineshchekov VA. Applications of fluorescence spectroscopy in the investigation of plant phytochrome invivo. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108434. [PMID: 38412703 DOI: 10.1016/j.plaphy.2024.108434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
Fluorometry is an effective research tool in biology and medicine; it is widely used in the study of the photosynthetic pigment apparatus in vivo. This method can be applied to the key plant photoreceptor phytochrome (phy). The fluorescence of phytochrome in plants was recorded for the first time in the group of the author, and a spectrofluorometric technique for its in vivo study was developed. The photophysical and photochemical properties of the pigment were described, and the photoreceptor was shown to be present in plants as two phenomenological types-active (at cryogenic temperatures) and water-soluble (Pr') and inactive and amphiphilic (Pr″). The scheme of the photoreaction explaining their photochemical distinctions was proposed. Phytochrome A was shown to comprise both types (phyA' and phyA″), whereas phytochrome B was only the second type. For phyA', distinct conformers have been detected. phyA' and phyA″ differ by the N-terminus of the molecule, possibly by serine phosphorylation. They mediate, respectively, the very low fluence and high irradiance photoresponses. Light, internal factors (kinase/phosphatase balance, pH), and hormones (jasmonate) were shown to affect the content and functions of the two phyA pools. All this points to the effectiveness of the developed method for invivo investigations of the phytochrome system. The data obtained can be applied in practical terms in agrobiology and light culture, as well as in the use of phytochrome as a new nanotool and a fluorescent probe.
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Affiliation(s)
- V A Sineshchekov
- Biology Department, M. V. Lomonosov Moscow State University, Moscow, 119234, Russia.
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Pashkovskiy P, Khalilova L, Vereshchagin M, Voronkov A, Ivanova T, Kosobryukhov AA, Allakhverdiev SI, Kreslavski VD, Kuznetsov VV. Impact of varying light spectral compositions on photosynthesis, morphology, chloroplast ultrastructure, and expression of light-responsive genes in Marchantia polymorpha. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108044. [PMID: 37776673 DOI: 10.1016/j.plaphy.2023.108044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/18/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
Marchantia polymorpha is a convenient model for studying light of different spectral compositions on various physiological and biochemical processes because its photoreceptor system is vastly simplified. The influence of red light (RL, 660 nm), far-red light (FRL, 730 nm), blue light (BL, 450 nm), and green light (GL, 525 nm) compared to white light (high-pressure sodium light (HPSL), white LEDs (WL 450 + 580 nm) and white fluorescent light (WFL) on photosynthetic and transpiration rates, photosystem II (PSII) activity, photomorphogenesis, and the expression of light and hormonal signaling genes was studied. The ultrastructure of the chloroplasts in different tissues of the gametophyte M. polymorpha was examined. FRL led to the formation of agranal chloroplasts (in the epidermis and the chlorenchyma) with a high starch content (in the parenchyma), which led to a reduced intensity of photosynthesis. BL increased the transcription of genes for the biosynthesis of secondary metabolites - chalcone synthase (CHS), cellulose synthase (CELL), and L-ascorbate peroxidase (APOX3), which is consistent with the increased activity of low-molecular weight antioxidants. FRL increased the expression of phytochrome apoprotein (PHY) and cytokinin oxidase (CYTox) genes, but the expression of the phytochrome interacting factor (PIF) gene decreased, which was accompanied by a significant change in gametophyte morphology. Analysis of crosstalk gene expression, and changes in morphology and photosynthetic activity was carried out.
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Affiliation(s)
- Pavel Pashkovskiy
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
| | - Lyudmila Khalilova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
| | - Mikhail Vereshchagin
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
| | - Alexander Voronkov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
| | - Tatiana Ivanova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
| | - Anatoliy A Kosobryukhov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, 142290, Russia.
| | - Suleyman I Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
| | - Vladimir D Kreslavski
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, 142290, Russia.
| | - Vladimir V Kuznetsov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
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Cannon AE, Sabharwal T, Salmi ML, Chittari GK, Annamalai V, Leggett L, Morris H, Slife C, Clark G, Roux SJ. Two distinct light-induced reactions are needed to promote germination in spores of Ceratopteris richardii. FRONTIERS IN PLANT SCIENCE 2023; 14:1150199. [PMID: 37332704 PMCID: PMC10272463 DOI: 10.3389/fpls.2023.1150199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Germination of Ceratopteris richardii spores is initiated by light and terminates 3-4 days later with the emergence of a rhizoid. Early studies documented that the photoreceptor for initiating this response is phytochrome. However, completion of germination requires additional light input. If no further light stimulus is given after phytochrome photoactivation, the spores do not germinate. Here we show that a crucial second light reaction is required, and its function is to activate and sustain photosynthesis. Even in the presence of light, blocking photosynthesis with DCMU after phytochrome photoactivation blocks germination. In addition, RT-PCR showed that transcripts for different phytochromes are expressed in spores in darkness, and the photoactivation of these phytochromes results in the increased transcription of messages encoding chlorophyll a/b binding proteins. The lack of chlorophyll-binding protein transcripts in unirradiated spores and their slow accumulation makes it unlikely that photosynthesis is required for the initial light reaction. This conclusion is supported by the observation that the transient presence of DCMU, only during the initial light reaction, had no effect on germination. Additionally, the [ATP] in Ceratopteris richardii spores increased coincidentally with the length of light treatment during germination. Overall, these results support the conclusion that two distinct light reactions are required for the germination of Ceratopteris richardii spores.
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Phokas A, Meyberg R, Briones‐Moreno A, Hernandez‐Garcia J, Wadsworth PT, Vesty EF, Blazquez MA, Rensing SA, Coates JC. DELLA proteins regulate spore germination and reproductive development in Physcomitrium patens. THE NEW PHYTOLOGIST 2023; 238:654-672. [PMID: 36683399 PMCID: PMC10952515 DOI: 10.1111/nph.18756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Proteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding 'Green Revolution' dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. We have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). PpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss-specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as 'hubs' for transcriptional regulation similarly to their homologues across the plant kingdom. Taken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.
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Affiliation(s)
- Alexandros Phokas
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8Marburg35043Germany
| | - Asier Briones‐Moreno
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | - Jorge Hernandez‐Garcia
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | | | - Eleanor F. Vesty
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
| | - Miguel A. Blazquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | - Stefan A. Rensing
- Faculty of Chemistry and PharmacyUniversity of FreiburgStefan‐Meier‐Straße 19Freiburg79104Germany
| | - Juliet C. Coates
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
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6
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Kreiss M, Haas FB, Hansen M, Rensing SA, Hoecker U. Co-action of COP1, SPA and cryptochrome in light signal transduction and photomorphogenesis of the moss Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:159-175. [PMID: 36710658 DOI: 10.1111/tpj.16128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The Arabidopsis COP1/SPA ubiquitin ligase suppresses photomorphogenesis in darkness. In the light, photoreceptors inactivate COP1/SPA to allow a light response. While SPA genes are specific to the green lineage, COP1 also exists in humans. This raises the question of when in evolution plant COP1 acquired the need for SPA accessory proteins. We addressed this question by generating Physcomitrium Ppcop1 mutants and comparing their visible and molecular phenotypes with those of Physcomitrium Ppspa mutants. The phenotype of Ppcop1 nonuple mutants resembles that of Ppspa mutants. Most importantly, both mutants produce green chloroplasts in complete darkness. They also exhibit dwarfed gametophores, disturbed branching of protonemata and absent gravitropism. RNA-sequencing analysis indicates that both mutants undergo weak constitutive light signaling in darkness. PpCOP1 and PpSPA proteins form a complex and they interact via their WD repeat domains with the VP motif of the cryptochrome CCE domain in a blue light-dependent manner. This resembles the interaction of Arabidopsis SPA proteins with Arabidopsis CRY1, and is different from that with Arabidopsis CRY2. Taken together, the data indicate that PpCOP1 and PpSPA act together to regulate growth and development of Physcomitrium. However, in contrast to their Arabidopsis orthologs, PpCOP1 and PpSPA proteins execute only partial suppression of light signaling in darkness. Hence, additional repressors may exist that contribute to the repression of a light response in dark-exposed Physcomitrium.
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Affiliation(s)
- Melanie Kreiss
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Maike Hansen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany
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7
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Zhou Y, Kong D, Wang X, Yu G, Wu X, Guan N, Weber W, Ye H. A small and highly sensitive red/far-red optogenetic switch for applications in mammals. Nat Biotechnol 2022; 40:262-272. [PMID: 34608325 DOI: 10.1038/s41587-021-01036-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Optogenetic technologies have transformed our ability to precisely control biological processes in time and space. Yet, current eukaryotic optogenetic systems are limited by large or complex optogenetic modules, long illumination times, low tissue penetration or slow activation and deactivation kinetics. Here, we report a red/far-red light-mediated and miniaturized Δphytochrome A (ΔPhyA)-based photoswitch (REDMAP) system based on the plant photoreceptor PhyA, which rapidly binds the shuttle protein far-red elongated hypocotyl 1 (FHY1) under illumination with 660-nm light with dissociation occurring at 730 nm. We demonstrate multiple applications of REDMAP, including dynamic on/off control of the endogenous Ras/Erk mitogen-activated protein kinase (MAPK) cascade and control of epigenetic remodeling using a REDMAP-mediated CRISPR-nuclease-deactivated Cas9 (CRISPR-dCas9) (REDMAPcas) system in mice. We also demonstrate the utility of REDMAP tools for in vivo applications by activating the expression of transgenes delivered by adeno-associated viruses (AAVs) or incorporated into cells in microcapsules implanted into mice, rats and rabbits illuminated by light-emitting diodes (LEDs). Further, we controlled glucose homeostasis in type 1 diabetic (T1D) mice and rats using REDMAP to trigger insulin expression. REDMAP is a compact and sensitive tool for the precise spatiotemporal control of biological activities in animals with applications in basic biology and potentially therapy.
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Affiliation(s)
- Yang Zhou
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xinyi Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Guiling Yu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ningzi Guan
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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Ríos-Meléndez S, Valadez-Hernández E, Delgadillo C, Luna-Guevara ML, Martínez-Núñez MA, Sánchez-Pérez M, Martínez-Y-Pérez JL, Arroyo-Becerra A, Cárdenas L, Bibbins-Martínez M, Maldonado-Mendoza IE, Villalobos-López MA. Pseudocrossidium replicatum (Taylor) R.H. Zander is a fully desiccation-tolerant moss that expresses an inducible molecular mechanism in response to severe abiotic stress. PLANT MOLECULAR BIOLOGY 2021; 107:387-404. [PMID: 34189708 PMCID: PMC8648698 DOI: 10.1007/s11103-021-01167-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 06/10/2021] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE The moss Pseudocrossidium replicatum is a desiccation-tolerant species that uses an inducible system to withstand severe abiotic stress in both protonemal and gametophore tissues. Desiccation tolerance (DT) is the ability of cells to recover from an air-dried state. Here, the moss Pseudocrossidium replicatum was identified as a fully desiccation-tolerant (FDT) species. Its gametophores rapidly lost more than 90% of their water content when exposed to a low-humidity atmosphere [23% relative humidity (RH)], but abscisic acid (ABA) pretreatment diminished the final water loss after equilibrium was reached. P. replicatum gametophores maintained good maximum photosystem II (PSII) efficiency (Fv/Fm) for up to two hours during slow dehydration; however, ABA pretreatment induced a faster decrease in the Fv/Fm. ABA also induced a faster recovery of the Fv/Fm after rehydration. Protein synthesis inhibitor treatment before dehydration hampered the recovery of the Fv/Fm when the gametophores were rehydrated after desiccation, suggesting the presence of an inducible protective mechanism that is activated in response to abiotic stress. This observation was also supported by accumulation of soluble sugars in gametophores exposed to ABA or NaCl. Exogenous ABA treatment delayed the germination of P. replicatum spores and induced morphological changes in protonemal cells that resembled brachycytes. Transcriptome analyses revealed the presence of an inducible molecular mechanism in P. replicatum protonemata that was activated in response to dehydration. This study is the first RNA-Seq study of the protonemal tissues of an FDT moss. Our results suggest that P. replicatum is an FDT moss equipped with an inducible molecular response that prepares this species for severe abiotic stress and that ABA plays an important role in this response.
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Affiliation(s)
- Selma Ríos-Meléndez
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Emmanuel Valadez-Hernández
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Claudio Delgadillo
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria L Luna-Guevara
- Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, C.P. 72000, Puebla, Puebla, México
| | - Mario A Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, C.P. 97302, Mérida, Yucatán, México
| | - Mishael Sánchez-Pérez
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, México
| | - José L Martínez-Y-Pérez
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, C.P. 90210, Ixtacuixtla, Tlaxcala, México
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Luis Cárdenas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, México
| | - Martha Bibbins-Martínez
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Ignacio E Maldonado-Mendoza
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, C.P. 81049, Guasave, Sinaloa, México
| | - Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México.
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9
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Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R. Development and Molecular Genetics of Marchantia polymorpha. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:677-702. [PMID: 33684298 DOI: 10.1146/annurev-arplant-082520-094256] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.
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Affiliation(s)
- Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Japan;
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
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10
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A LexA-based yeast two-hybrid system for studying light-switchable interactions of phytochromes with their interacting partners. ABIOTECH 2021; 2:105-116. [PMID: 36304755 PMCID: PMC9590525 DOI: 10.1007/s42994-021-00034-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022]
Abstract
Phytochromes are a family of photoreceptors in plants that perceive the red (R) and far-red (FR) components of their light environment. Phytochromes exist in vivo in two forms, the inactive Pr form and the active Pfr form, that are interconvertible by treatments with R or FR light. It is believed that phytochromes transduce light signals by interacting with their signaling partners. A GAL4-based light-switchable yeast two-hybrid (Y2H) system was developed two decades ago and has been successfully employed in many studies to determine phytochrome interactions with their signaling components. However, several pairs of interactions between phytochromes and their interactors, such as the phyA-COP1 and phyA-TZP interactions, were demonstrated by other assay systems but were not detected by this GAL4 Y2H system. Here, we report a modified LexA Y2H system, in which the LexA DNA-binding domain is fused to the C-terminus of a phytochrome protein. The conformational changes of phytochromes in response to R and FR light are achieved in yeast cells by exogenously supplying phycocyanobilin (PCB) extracted from Spirulina. The well-defined interaction pairs, including phyA-FHY1 and phyB-PIFs, are well reproducible in this system. Moreover, we show that our system is successful in detecting the phyA-COP1 and phyA-TZP interactions. Together, our study provides an alternative Y2H system that is highly sensitive and reproducible for detecting light-switchable interactions of phytochromes with their interacting partners. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00034-5.
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Cai S, Huang Y, Chen F, Zhang X, Sessa E, Zhao C, Marchant DB, Xue D, Chen G, Dai F, Leebens‐Mack JH, Zhang G, Shabala S, Christie JM, Blatt MR, Nevo E, Soltis PS, Soltis DE, Franks PJ, Wu F, Chen Z. Evolution of rapid blue-light response linked to explosive diversification of ferns in angiosperm forests. THE NEW PHYTOLOGIST 2021; 230:1201-1213. [PMID: 33280113 PMCID: PMC8048903 DOI: 10.1111/nph.17135] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/21/2020] [Indexed: 05/23/2023]
Abstract
Ferns appear in the fossil record some 200 Myr before angiosperms. However, as angiosperm-dominated forest canopies emerged in the Cretaceous period there was an explosive diversification of modern (leptosporangiate) ferns, which thrived in low, blue-enhanced light beneath angiosperm canopies. A mechanistic explanation for this transformative event in the diversification of ferns has remained elusive. We used physiological assays, transcriptome analysis and evolutionary bioinformatics to investigate a potential connection between the evolution of enhanced stomatal sensitivity to blue light in modern ferns and the rise of angiosperm-dominated forests in the geological record. We demonstrate that members of the largest subclade of leptosporangiate ferns, Polypodiales, have significantly faster stomatal response to blue light than more ancient fern lineages and a representative angiosperm. We link this higher sensitivity to levels of differentially expressed genes in blue-light signaling, particularly in the cryptochrome (CRY) signaling pathway. Moreover, CRYs of the Polypodiales examined show gene duplication events between 212.9-196.9 and 164.4-151.8 Ma, when angiosperms were emerging, which are lacking in other major clades of extant land plants. These findings suggest that evolution of stomatal blue-light sensitivity helped modern ferns exploit the shady habitat beneath angiosperm forest canopies, fueling their Cretaceous hyperdiversification.
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Affiliation(s)
- Shengguan Cai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
| | - Yuqing Huang
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
| | - Fei Chen
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Xin Zhang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Emily Sessa
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
| | - Chenchen Zhao
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - D. Blaine Marchant
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- Department of BiologyStanford UniversityStanfordCA94305USA
| | - Dawei Xue
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Guang Chen
- Collaborative Innovation Centre for Grain IndustryCollege of AgricultureYangtze UniversityJingzhou434025China
| | - Fei Dai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | | | - Guoping Zhang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Sergey Shabala
- Tasmanian Institute of AgricultureUniversity of TasmaniaHobartTAS7004Australia
- International Research Centre for Environmental Membrane BiologyFoshan UniversityFoshan528041China
| | - John M. Christie
- Laboratory of Plant Physiology and BiophysicsUniversity of GlasgowGlasgowG12 8QQUK
| | - Michael R. Blatt
- Laboratory of Plant Physiology and BiophysicsUniversity of GlasgowGlasgowG12 8QQUK
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaMount CarmelHaifa34988384Israel
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
| | - Douglas E. Soltis
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
| | - Peter J. Franks
- School of Life and Environmental SciencesThe University of SydneySydneyNSW2006Australia
| | - Feibo Wu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Zhong‐Hua Chen
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
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12
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Dijkhuizen LW, Tabatabaei BES, Brouwer P, Rijken N, Buijs VA, Güngör E, Schluepmann H. Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition. FRONTIERS IN PLANT SCIENCE 2021; 12:693039. [PMID: 34456937 PMCID: PMC8386757 DOI: 10.3389/fpls.2021.693039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/22/2021] [Indexed: 05/02/2023]
Abstract
Water ferns of the genus Azolla and the filamentous cyanobacteria Nostoc azollae constitute a model symbiosis that enabled the colonization of the water surface with traits highly desirable for the development of more sustainable crops: their floating mats capture CO2 and fix N2 at high rates using light energy. Their mode of sexual reproduction is heterosporous. The regulation of the transition from the vegetative phase to the spore forming phase in ferns is largely unknown, yet a prerequisite for Azolla domestication, and of particular interest as ferns represent the sister lineage of seed plants. Sporocarps induced with far red light could be crossed so as to verify species attribution of strains from the Netherlands but not of the strain from the Anzali lagoon in Iran; the latter strain was assigned to a novel species cluster from South America. Red-dominated light suppresses the formation of dissemination stages in both gametophyte- and sporophyte-dominated lineages of plants, the response likely is a convergent ecological strategy to open fields. FR-responsive transcripts included those from MIKCC homologues of CMADS1 and miR319-controlled GAMYB transcription factors in the fern, transporters in N. azollae, and ycf2 in chloroplasts. Loci of conserved microRNA (miRNA) in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159. Phylogenomic analyses of MIKCC TFs suggested that the control of flowering and flower organ specification may have originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.
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Affiliation(s)
- Laura W. Dijkhuizen
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Paul Brouwer
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Niels Rijken
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Valerie A. Buijs
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Erbil Güngör
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Henriette Schluepmann
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
- *Correspondence: Henriette Schluepmann
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13
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Biswal DP, Panigrahi KCS. Light- and hormone-mediated development in non-flowering plants: An overview. PLANTA 2020; 253:1. [PMID: 33245411 DOI: 10.1007/s00425-020-03501-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.
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Affiliation(s)
- Durga Prasad Biswal
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, India
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kishore Chandra Sekhar Panigrahi
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, India.
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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14
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Xu T, Yuan J, Hiltbrunner A. PHYTOCHROME INTERACTING FACTORs in the moss Physcomitrella patens regulate light-controlled gene expression. PHYSIOLOGIA PLANTARUM 2020; 169:467-479. [PMID: 32447760 DOI: 10.1111/ppl.13140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Phytochromes are red and far-red light receptors in plants that control growth and development in response to changes in the environment. Light-activated phytochromes enter the nucleus and act on a set of downstream signalling components to regulate gene expression. PHYTOCHROME INTERACTING FACTORs (PIFs) belong to the basic helix-loop-helix family of transcription factors and directly bind to light-activated phytochromes. Potential homologues of PIFs have been identified in ferns, bryophytes and streptophyte algae, and it has been shown that the potential PIF homologues from Physcomitrella patens, PIF1 to PIF4, have PIF function when expressed in Arabidopsis. However, their function in Physcomitrella is still unknown. Seed plant PIFs bind to G-box-containing promoters and, therefore, we searched the Physcomitrella genome for genes that contain G-boxes in their promoter. Here, we show that Physcomitrella PIFs activate these promoters in a G-box-dependent manner, suggesting that they could be direct PIF targets. Furthermore, we generated Physcomitrella pif1, pif2, pif3 and pif4 knock out mutant lines and quantified the expression of potential PIF direct target genes. The expression of these genes was generally reduced in pif mutants compared to the wildtype, but for several genes, the relative induction upon a short light treatment was higher in pif mutants than the wildtype. In contrast, expression of these genes was strongly repressed in continuous light, and pif mutants showed partial downregulation of these genes in the dark. Thus, the overall function of PIFs in light-regulated gene expression might be an ancient property of PIFs.
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Affiliation(s)
- Tengfei Xu
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinhong Yuan
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany
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15
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Bryophytes can recognize their neighbours through volatile organic compounds. Sci Rep 2020; 10:7405. [PMID: 32366980 PMCID: PMC7198583 DOI: 10.1038/s41598-020-64108-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/28/2020] [Indexed: 02/03/2023] Open
Abstract
Communication between vascular plants through volatile organic compounds (VOCs) impacts on ecosystem functioning. However, nothing is known about that between non-vascular plants. To investigate plant-plant VOCs interaction in bryophytes we exposed rare peatland moss Hamatocaulis vernicosus to VOCs of its common competitor Sphagnum flexuosum in an air-flow system of connected containers under artificial light, supplemented or unsupplemented by far-red (FR) light. When exposed to VOCs of S. flexuosum, shoots of H. vernicosus elongated and emitted six times higher amounts of a compound chemically related to β-cyclocitral, which is employed in stress signalling and allelopathy in vascular plants. The VOCs emission was affected similarly by FR light addition, possibly simulating competition stress. This is the first evidence of plant-plant VOCs interaction in non-vascular plants, analogous to that in vascular plants. The findings open new possibilities for understanding the language and evolution of communication in land plants.
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16
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Menon C, Klose C, Hiltbrunner A. Arabidopsis FHY1 and FHY1-LIKE Are Not Required for Phytochrome A Signal Transduction in the Nucleus. PLANT COMMUNICATIONS 2020; 1:100007. [PMID: 33404546 PMCID: PMC7748001 DOI: 10.1016/j.xplc.2019.100007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/27/2019] [Accepted: 11/06/2019] [Indexed: 05/13/2023]
Abstract
Photoreceptors of the phytochrome family control a multitude of responses in plants. Phytochrome A (phyA) is essential for far-red light perception, which is important for germination and seedling establishment in strong canopy shade. Translocation of phyA from the cytosol into nucleus is a key step in far-red light signaling and requires FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). FHY1/FHL bind to phyA downstream signaling components. Therefore, it has been suggested that FHY1/FHL also have a function in assembling phyA transcription factor complexes in the nucleus. Yet, in this study, we show that constitutively nuclear-localized phyA is active in the absence of FHY1 and FHL. Furthermore, an artificial FHY1, consisting of an SV40 NLS, a phyA binding site, and a YFP tag as spacer between them, complements the fhy1-3 fhl-1 double mutant. These findings show that FHY1 and FHL are not required for phyA downstream signaling in the nucleus. However, we found that lines expressing phyA-NLS-YFP are hypersensitive to red and far-red light and that slightly increased levels of constitutively nuclear-localized phyA result in photomorphogenic development in the dark. Thus, restricting phyA to the cytosol and inducing nuclear transport in light by interaction with FHY1/FHL might be important to suppress photomorphogenesis in the dark.
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Affiliation(s)
- Chiara Menon
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Cornelia Klose
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Corresponding author
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17
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Lin BY, Shih CJ, Hsieh HY, Chen HC, Tu SL. Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer. PLANT PHYSIOLOGY 2020; 182:243-254. [PMID: 31501299 PMCID: PMC6945828 DOI: 10.1104/pp.19.00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/24/2019] [Indexed: 05/25/2023]
Abstract
Plants perceive environmental light conditions and optimize their growth and development accordingly by regulating gene activity at multiple levels. Photoreceptors are important for light sensing and downstream gene regulation. Phytochromes, red/far-red light receptors, are believed to regulate light-responsive alternative splicing, but little is known about the underlying mechanism. Alternative splicing is primarily regulated by transacting factors, such as splicing regulators, and by cis-acting elements in precursor mRNA. In the moss Physcomitrella patens, we show that phytochrome 4 (PpPHY4) directly interacts with a splicing regulator, heterogeneous nuclear ribonucleoprotein F1 (PphnRNP-F1), in the nucleus to regulate light-responsive alternative splicing. RNA sequencing analysis revealed that PpPHY4 and PphnRNP-F1 coregulate 70% of intron retention (IR) events in response to red light. A repetitive GAA motif was identified to be an exonic splicing silencer that controls red light-responsive IR. Biochemical studies indicated that PphnRNP-F1 is recruited by the GAA motif to form RNA-protein complexes. Finally, red light elevates PphnRNP-F1 protein levels via PpPHY4, increasing levels of IR. We propose that PpPHY4 and PphnRNP-F1 regulate alternative splicing through an exonic splicing silencer to control splicing machinery activity in response to light.
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Affiliation(s)
- Bou-Yun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Chueh-Ju Shih
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsin-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsiu-Chen Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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18
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Artz O, Dickopf S, Ranjan A, Kreiss M, Abraham ET, Boll V, Rensing SA, Hoecker U. Characterization of spa mutants in the moss Physcomitrella provides evidence for functional divergence of SPA genes during the evolution of land plants. THE NEW PHYTOLOGIST 2019; 224:1613-1626. [PMID: 31222750 DOI: 10.1111/nph.16004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.
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Affiliation(s)
- Oliver Artz
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stephen Dickopf
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Aashish Ranjan
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Melanie Kreiss
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Elena Theres Abraham
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Vanessa Boll
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
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19
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Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nat Commun 2019; 10:5219. [PMID: 31745087 PMCID: PMC6864062 DOI: 10.1038/s41467-019-13045-0] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 10/17/2019] [Indexed: 11/08/2022] Open
Abstract
Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.
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20
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Lee JW, Kim GH. Red And far-red regulation of filament movement correlates with the expression of phytochrome and FHY1 genes in Spirogyra varians (Zygnematales, Streptophyta) 1. JOURNAL OF PHYCOLOGY 2019; 55:688-699. [PMID: 30805922 DOI: 10.1111/jpy.12849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Spirogyra filaments show unique photomovement that differs in response to blue, red, and far-red light. Phototropins involved in the blue-light movement have been characterized together with downstream signaling components, but the photoreceptors and mechanical effectors of red- and far-red light movement are not yet characterized. The filaments of Spirogyra varians slowly bent and aggregated to form a tangled mass in red light. In far-red light, the filaments unbent, stretched rapidly, and separated from each other. Mannitol and/or sorbitol treatment significantly inhibited this far-red light movement suggesting that turgor pressure is the driving force of this movement. The bending and aggregating movements of filaments in red light were not affected by osmotic change. Three phytochrome homologues isolated from S. varians showed unique phylogenetic characteristics. Two canonical phytochromes, named SvPHY1 and SvPHY2, and a noncanonical phytochrome named SvPHYX2. SvPHY1 is the first PHY1 family phytochrome reported in zygnematalean algae. The gene involved in the transport of phytochromes into the nucleus was characterized, and its expression in response to red and far-red light was measured using quantitative PCR. Our results suggest that the phytochromes and the genes involved in the transport system into the nucleus are well conserved in S. varians.
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Affiliation(s)
- Ji Woong Lee
- Department of Biological Sciences, Kongju National University, Gongju, 32588, Korea
| | - Gwang Hoon Kim
- Department of Biological Sciences, Kongju National University, Gongju, 32588, Korea
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21
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Inoue K, Nishihama R, Araki T, Kohchi T. Reproductive Induction is a Far-Red High Irradiance Response that is Mediated by Phytochrome and PHYTOCHROME INTERACTING FACTOR in Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2019; 60:1136-1145. [PMID: 30816950 DOI: 10.1093/pcp/pcz029] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/08/2019] [Indexed: 05/15/2023]
Abstract
Land plants have evolved a series of photoreceptors to precisely perceive environmental information. Among these, phytochromes are the sole photoreceptors for red light (R) and far-red light (FR), and play pivotal roles in modulating various developmental processes. Most extant land plants possess multiple phytochromes that probably evolved from a single phytochrome in the common ancestor of land plants. However, the ancestral phytochrome signaling mechanism remains unknown due to a paucity of knowledge regarding phytochrome functions in basal land plants. It has recently been reported that Mpphy, a single phytochrome in the liverwort Marchantia polymorpha, regulates typical photoreversible responses collectively classified as low fluence response (LFR). Here, we show that Mpphy also regulates the gametangiophore formation analogous to the mode of action of the far-red high irradiance response (FR-HIR) in angiosperms. Our phenotypic analyses using mutant plants obtained by CRISPR/Cas9-based genome editing revealed that MpFHY1, an ortholog of FAR-RED ELONGATED HYPOCOTYL1, as well as Mpphy is critical for the FR-HIR signaling in M. polymorpha. In addition, knockout of MpPIF, a single PHYTOCHROME INTERACTING FACTOR gene in M. polymorpha, completely abolished the FR-HIR-dependent gametangiophore formation, while overexpression of MpPIF accelerated the response. FR-HIR-dependent transcriptional regulation was also disrupted in the Mppif mutant. Our findings suggest that plants had already acquired the FR-HIR signaling mediated by phytochrome and PIF at a very early stage during the course of land plant evolution, and that a single phytochrome in the common ancestor of land plants could mediate both LFR and FR-HIR.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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22
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Sineshchekov V. Two molecular species of phytochrome A with distinct modes of action. FUNCTIONAL PLANT BIOLOGY 2019; 46:118. [DOI: https:/doi.org/10.1071/fp18156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Adaptation of plants to environmental light conditions is achieved via operation of a highly complex photoreceptor apparatus. It includes the phytochrome system comprising phytochromes A and B (phyA and phyB) as the major components. phyA differs from phyB by several properties, including its ability to mediate all three photoresponse modes – the very low and low fluence responses (VLFR and LFR respectively) and the high irradiance responses (HIR), whereas phyB is responsible for LFR. This review discusses the uniqueness of phyA in terms of its structural and functional heterogeneity. The photoreceptor is presented in monocots and dicots by two native molecular species, phyAʹ and phyAʹʹ, differing by spectroscopic, photochemical and phenomenological properties. phyA differentiation into substates includes post-translational phosphorylation of a serine residue(s) at the N-terminal extension of the molecule with phyAʹ being the phosphorylated species and phyAʹʹ, dephosphorylated. They differ also by their mode of action, which depends on the cellular context. The current working hypothesis is that phyAʹ mediates VLFR and phyAʹʹ, HIR and LFR. The content and functional activity of the two pools are regulated by light and by phosphatase/kinase equilibrium and pH in darkness, what contributes to the fine-tuning of the phytochrome system. Detection of the native pools of the cryptogamic plant fern Adiantum capillus-veneris phy1 (phy1ʹ and phy1ʹʹ) similar to those of phyA suggests that the structural and functional heterogeneity of phyA is not a unique phenomenon and may have arisen earlier in the molecular evolution of the phytochrome system than the appearance of the angiosperm phytochromes.
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Sineshchekov V. Two molecular species of phytochrome A with distinct modes of action. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:118-135. [PMID: 32172754 DOI: 10.1071/fp18156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/17/2018] [Indexed: 06/10/2023]
Abstract
Adaptation of plants to environmental light conditions is achieved via operation of a highly complex photoreceptor apparatus. It includes the phytochrome system comprising phytochromes A and B (phyA and phyB) as the major components. phyA differs from phyB by several properties, including its ability to mediate all three photoresponse modes - the very low and low fluence responses (VLFR and LFR respectively) and the high irradiance responses (HIR), whereas phyB is responsible for LFR. This review discusses the uniqueness of phyA in terms of its structural and functional heterogeneity. The photoreceptor is presented in monocots and dicots by two native molecular species, phyA' and phyA'', differing by spectroscopic, photochemical and phenomenological properties. phyA differentiation into substates includes post-translational phosphorylation of a serine residue(s) at the N-terminal extension of the molecule with phyA' being the phosphorylated species and phyA'', dephosphorylated. They differ also by their mode of action, which depends on the cellular context. The current working hypothesis is that phyA' mediates VLFR and phyA'', HIR and LFR. The content and functional activity of the two pools are regulated by light and by phosphatase/kinase equilibrium and pH in darkness, what contributes to the fine-tuning of the phytochrome system. Detection of the native pools of the cryptogamic plant fern Adiantum capillus-veneris phy1 (phy1' and phy1'') similar to those of phyA suggests that the structural and functional heterogeneity of phyA is not a unique phenomenon and may have arisen earlier in the molecular evolution of the phytochrome system than the appearance of the angiosperm phytochromes.
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Affiliation(s)
- V Sineshchekov
- Biology Department, M.V. Lomonosov Moscow State University, Moscow, Russia. Email
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Ermert AL, Nogué F, Stahl F, Gans T, Hughes J. CRISPR/Cas9-Mediated Knockout of Physcomitrella patens Phytochromes. Methods Mol Biol 2019; 2026:237-263. [PMID: 31317418 DOI: 10.1007/978-1-4939-9612-4_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Here we describe procedures for gene disruption and excision in Physcomitrella using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated 9) methods, exemplarily targeting phytochrome (PHY) gene loci. Thereby double-strand breaks (DSBs) are induced using a single guide RNA (sgRNA) with the Cas9 nuclease, leading to insertions or deletions (indels) due to incorrect repair by the nonhomologous-end joining (NHEJ) mechanism. We also include protocols for excision of smaller genomic fragments or whole genes either with or without homologous recombination-assisted repair. The protocol can be adapted to target several loci simultaneously, thereby allowing the physiological analysis of phenotypes that would be masked by functional redundancy. In our particular case, multiple PHY gene knockouts would likely be valuable in understanding phytochrome functions in mosses and, perhaps, higher plants too. Target sites for site-directed induction of DSBs are predicted with the CRISPOR online-tool and are inserted in silico into sequence matrices for the design of sgRNA expression cassettes. The resulting DNAs are cloned into Gateway DONOR vectors and the respective expression plasmids used for moss cotransformation with a Cas9 expression plasmid and a selectable marker (either on a separate plasmid or on one of the other plasmids). After the selection process, genomic DNA is extracted and transformants are analyzed by PCR fingerprinting.
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Affiliation(s)
- Anna Lena Ermert
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
| | - Fabian Stahl
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Tanja Gans
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Jon Hughes
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany.
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Zhang S, Li C, Zhou Y, Wang X, Li H, Feng Z, Chen H, Qin G, Jin D, Terzaghi W, Gu H, Qu LJ, Kang D, Deng XW, Li J. TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling. THE PLANT CELL 2018; 30:835-852. [PMID: 29588390 PMCID: PMC5973844 DOI: 10.1105/tpc.17.00677] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/19/2018] [Accepted: 03/24/2018] [Indexed: 05/17/2023]
Abstract
Phytochrome A (phyA) is the primary plant photoreceptor responsible for perceiving and mediating various responses to far-red (FR) light and is essential for survival in canopy shade. In this study, we identified two Arabidopsis thaliana mutants that grew longer hypocotyls in FR light. Genetic analyses showed that they were allelic and their FR phenotypes were caused by mutations in the gene named TANDEM ZINC-FINGER/PLUS3 (TZP), previously shown to encode a nuclear protein involved in blue light signaling and phyB-dependent regulation of photoperiodic flowering. We show that the expression of TZP is dramatically induced by light and that TZP proteins are differentially modified in different light conditions. Furthermore, we show that TZP interacts with both phyA and FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and regulates the abundance of phyA, FHY1, and ELONGATED HYPOCOTYL5 proteins in FR light. Moreover, our data indicate that TZP is required for the formation of a phosphorylated form of phyA in the nucleus in FR light. Together, our results identify TZP as a positive regulator of phyA signaling required for phosphorylation of the phyA photoreceptor, thus suggesting an important role of phosphorylated phyA in inducing the FR light response.
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Affiliation(s)
- Shaoman Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Cong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoji Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziyi Feng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dan Jin
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dingming Kang
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Pham VN, Kathare PK, Huq E. Phytochromes and Phytochrome Interacting Factors. PLANT PHYSIOLOGY 2018; 176:1025-1038. [PMID: 29138351 PMCID: PMC5813575 DOI: 10.1104/pp.17.01384] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 05/18/2023]
Abstract
The basic helix-loop-helix domain-containing transcription factors that interact physically with the red and far-red light photoreceptors, phytochromes, are called PHYTOCHROME INTERACTING FACTORS (PIFs). In the last two decades, the phytochrome-PIF signaling module has been shown to be conserved from Physcomitrella patens to higher plants. Exciting recent studies highlight the discovery of at least four distinct kinases (PPKs, CK2, BIN2, and phytochrome itself) and four families of ubiquitin ligases (SCFEBF1/2, CUL3LRB, CUL3BOP, and CUL4COP1-SPA) that regulate PIF abundance both in dark and light conditions. This review discusses these recent discoveries with a focus on the central phytochrome signaling mechanisms that have a profound impact on plant growth and development in response to light.
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Affiliation(s)
- Vinh Ngoc Pham
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Enamul Huq
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
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Sineshchekov VA, Koppel LA, Bolle C. Two native types of phytochrome A, phyAʹ and phyAʺ, differ by the state of phosphorylation at the N-terminus as revealed by fluorescence investigations of the Ser/Ala mutant of rice phyA expressed in transgenic Arabidopsis. FUNCTIONAL PLANT BIOLOGY 2018; 45:150. [DOI: https:/doi.org/10.1071/fp16261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Phytochrome A (phyA) mediates different photoresponses what may be connected with the existence of its two types, phyAʹ and phyAʹʹ, differing by spectroscopic, photochemical and functional properties. We investigated a role of phyA phosphorylation in their formation turning to transgenic Arabidopsis thaliana (L. Heynh.) phyA or phyAphyB mutants overexpressing rice wild-type phyA (phyA WT) or mutant phyA (phyA SA) with the first 10 serines substituted by alanines. This prevents phyA phosphorylation at these sites and modifies photoresponses. Etiolated seedlings were employed and phyA parameters were evaluated with the use of low temperature fluorescence spectroscopy and photochemistry. Germination of seeds was induced by white light (WL) pre-treatment for 15 min or 3 h. Emission spectra of rice phyA WT and phyA SA were similar and their total content was comparable. However, the phyAʹ/phyAʹʹ proportion in phyA WT was high and varied with the duration of the WL pre-treatment, whereas in phyA SA it was substantially shifted towards phyAʹʹ and did not depend on the pre-illumination. This suggests that phyA SA comprises primarily or exclusively the phyAʹʹ pool and supports the notion that the two phyA types differ by the state of serine phosphorylation. phyAʹʹ was also found to be much more effective in the germination induction than phyAʹ.
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Sineshchekov VA, Koppel LA, Bolle C. Two native types of phytochrome A, phyA' and phyA", differ by the state of phosphorylation at the N-terminus as revealed by fluorescence investigations of the Ser/Ala mutant of rice phyA expressed in transgenic Arabidopsis. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:150-159. [PMID: 32291029 DOI: 10.1071/fp16261] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 11/01/2016] [Indexed: 06/11/2023]
Abstract
Phytochrome A (phyA) mediates different photoresponses what may be connected with the existence of its two types, phyA' and phyA'', differing by spectroscopic, photochemical and functional properties. We investigated a role of phyA phosphorylation in their formation turning to transgenic Arabidopsis thaliana (L. Heynh.) phyA or phyAphyB mutants overexpressing rice wild-type phyA (phyA WT) or mutant phyA (phyA SA) with the first 10 serines substituted by alanines. This prevents phyA phosphorylation at these sites and modifies photoresponses. Etiolated seedlings were employed and phyA parameters were evaluated with the use of low temperature fluorescence spectroscopy and photochemistry. Germination of seeds was induced by white light (WL) pre-treatment for 15min or 3h. Emission spectra of rice phyA WT and phyA SA were similar and their total content was comparable. However, the phyA'/phyA'' proportion in phyA WT was high and varied with the duration of the WL pre-treatment, whereas in phyA SA it was substantially shifted towards phyA'' and did not depend on the pre-illumination. This suggests that phyA SA comprises primarily or exclusively the phyA'' pool and supports the notion that the two phyA types differ by the state of serine phosphorylation. phyA'' was also found to be much more effective in the germination induction than phyA'.
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Affiliation(s)
| | - Larissa A Koppel
- Biology Department, MV Lomonosov Moscow State University, Moscow 119234, Russia
| | - Cordelia Bolle
- Biology Department, Ludwig Maximilian University, München, D-82152 Planegg-Martinsried, Germany
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Xu T, Hiltbrunner A. PHYTOCHROME INTERACTING FACTORs from Physcomitrella patens are active in Arabidopsis and complement the pif quadruple mutant. PLANT SIGNALING & BEHAVIOR 2017; 12:e1388975. [PMID: 28985148 PMCID: PMC5703237 DOI: 10.1080/15592324.2017.1388975] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
Phytochromes are red/far-red light receptors in plants involved in the regulation of growth and development in response to changes in the ambient environment. An important mode of action of plant phytochromes depends on their light-regulated relocation from the cytosol into the nucleus and control of gene expression; in addition, there is also evidence for a cytosolic or plasma membrane associated function of phytochromes in different species. The PHYTOCHROME INTERACTING FACTORs (PIFs) form a subgroup of the bHLH transcription factors and it is well established that PIFs are key components of phytochrome downstream signalling in the nucleus of seed plants. Recent studies identified members of the PIF family also in the liverwort Marchantia polymorpha and the moss Physcomitrella patens. Here, we show that all four potential PIF homologs from Physcomitrella have PIF function when expressed in the Arabidopsis pifQ mutant, which is deficient in multiple PIFs. We propose that PIFs are ancient components of nuclear phytochrome signalling that have emerged in the last common ancestor of today's land plants.
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Affiliation(s)
- Tengfei Xu
- Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- CONTACT Andreas Hiltbrunner Institute of Biology II, Schänzlestrasse 1, 79104 Freiburg, Germany
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Sheerin DJ, Hiltbrunner A. Molecular mechanisms and ecological function of far-red light signalling. PLANT, CELL & ENVIRONMENT 2017; 40:2509-2529. [PMID: 28102581 DOI: 10.1111/pce.12915] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 05/18/2023]
Abstract
Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.
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Affiliation(s)
- David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
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31
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Inoue K, Nishihama R, Kohchi T. Evolutionary origin of phytochrome responses and signaling in land plants. PLANT, CELL & ENVIRONMENT 2017; 40:2502-2508. [PMID: 28098347 DOI: 10.1111/pce.12908] [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] [Received: 10/14/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 06/06/2023]
Abstract
Phytochromes comprise one of the major photoreceptor families in plants, and they regulate many aspects of plant growth and development throughout the plant life cycle. A canonical land plant phytochrome originated in the common ancestor of streptophytes. Phytochromes have diversified in seed plants and some basal land plants because of lineage-specific gene duplications that occurred during the course of land plant evolution. Molecular genetic analyses using Arabidopsis thaliana suggested that there are two types of phytochromes in angiosperms, light-labile type I and light-stable type II, which have different signaling mechanisms and which regulate distinct responses. In basal land plants, little is known about molecular mechanisms of phytochrome signaling, although red light/far-red photoreversible physiological responses and the distribution of phytochrome genes are relatively well documented. Recent advances in molecular genetics using the moss Physcomitrella patens and the liverwort Marchantia polymorpha revealed that basal land plants show far-red-induced responses and that the establishment of phytochrome-mediated transcriptional regulation dates back to at least the common ancestor of land plants. In this review, we summarize our knowledge concerning functions of land plant phytochromes, especially in basal land plants, and discuss subfunctionalization/neofunctionalization of phytochrome signaling during the course of land plant evolution.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
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Hiss M, Meyberg R, Westermann J, Haas FB, Schneider L, Schallenberg-Rüdinger M, Ullrich KK, Rensing SA. Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:606-620. [PMID: 28161906 DOI: 10.1111/tpj.13501] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 05/21/2023]
Abstract
Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences, and to investigate the effects of environmental adaption and acclimation. For the model moss Physcomitrella patens collections of accessions are available, and have been used for phylogenetic and taxonomic studies, for example, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing. We analysed cross-technology and cross-laboratory data to define a confident set of 15 mature sporophyte-specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes than Reute or Villersexel, although gametangia develop with the same time course and do not show evident morphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet we found variation between Gransden and Reute in the expression profiles of several genes, as well as variation hot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression differences between the ecotypes for selected candidate genes in the GRAS transcription factor family, the chalcone synthase family and in genes involved in cell wall modification that are potentially related to phenotypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse-genetics studies that involve progression through the life cycle and multiple generations.
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Affiliation(s)
- Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Jens Westermann
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | | | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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Possart A, Xu T, Paik I, Hanke S, Keim S, Hermann HM, Wolf L, Hiß M, Becker C, Huq E, Rensing SA, Hiltbrunner A. Characterization of Phytochrome Interacting Factors from the Moss Physcomitrella patens Illustrates Conservation of Phytochrome Signaling Modules in Land Plants. THE PLANT CELL 2017; 29:310-330. [PMID: 28123107 PMCID: PMC5354185 DOI: 10.1105/tpc.16.00388] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 12/22/2016] [Accepted: 01/22/2017] [Indexed: 05/19/2023]
Abstract
Across the plant kingdom, phytochrome (PHY) photoreceptors play an important role during adaptive and developmental responses to light. In Arabidopsis thaliana, light-activated PHYs accumulate in the nucleus, where they regulate downstream signaling components, such as phytochrome interacting factors (PIFs). PIFs are transcription factors that act as repressors of photomorphogenesis; their inhibition by PHYs leads to substantial changes in gene expression. The nuclear function of PHYs, however, has so far been investigated in only a few non-seed plants. Here, we identified putative target genes of PHY signaling in the moss Physcomitrella patens and found light-regulated genes that are putative orthologs of PIF-controlled genes in Arabidopsis. Phylogenetic analyses revealed that an ancestral PIF-like gene was already present in streptophyte algae, i.e., before the water-to-land transition of plants. The PIF homologs in the genome of P. patens resemble Arabidopsis PIFs in their protein domain structure, molecular properties, and physiological effects, albeit with notable differences in the motif-dependent PHY interaction. Our results suggest that P. patens PIFs are involved in PHY signaling. The PHY-PIF signaling node that relays light signals to target genes has been largely conserved during land plant evolution, with evidence of lineage-specific diversification.
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Affiliation(s)
- Anja Possart
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Tengfei Xu
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Inyup Paik
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Sebastian Hanke
- Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Sarah Keim
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Helen-Maria Hermann
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Luise Wolf
- Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Manuel Hiß
- Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Stefan A Rensing
- Faculty of Biology, University of Marburg, 35043 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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34
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Lee N, Choi G. Phytochrome-interacting factor from Arabidopsis to liverwort. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:54-60. [PMID: 27875778 DOI: 10.1016/j.pbi.2016.11.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 05/08/2023]
Abstract
Phytochromes are red and far-red light photoreceptors that regulate the responses of plants to light throughout their life cycles. Phytochromes do this in part by inhibiting the function of a group of basic helix-loop-helix transcription factors called phytochrome-interacting factors (PIFs). Arabidopsis has eight PIFs that function sometimes redundantly and sometimes distinctively depending on their expression patterns and protein stability, as well as on variations in the promoters they target in vivo. PIF-like proteins exist in other seed plants and non-vascular plants where they also regulate light responses. The mechanism by which phytochrome regulates light responses by promoting the degradation of the PIFs is conserved in liverwort, suggesting it must have evolved some time before the last common ancestor shared by seed plants and non-vascular plants.
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Affiliation(s)
- Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea.
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35
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Vesty EF, Saidi Y, Moody LA, Holloway D, Whitbread A, Needs S, Choudhary A, Burns B, McLeod D, Bradshaw SJ, Bae H, King BC, Bassel GW, Simonsen HT, Coates JC. The decision to germinate is regulated by divergent molecular networks in spores and seeds. THE NEW PHYTOLOGIST 2016; 211:952-66. [PMID: 27257104 PMCID: PMC4950004 DOI: 10.1111/nph.14018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/16/2016] [Indexed: 05/15/2023]
Abstract
Dispersal is a key step in land plant life cycles, usually via formation of spores or seeds. Regulation of spore- or seed-germination allows control over the timing of transition from one generation to the next, enabling plant dispersal. A combination of environmental and genetic factors determines when seed germination occurs. Endogenous hormones mediate this decision in response to the environment. Less is known about how spore germination is controlled in earlier-evolving nonseed plants. Here, we present an in-depth analysis of the environmental and hormonal regulation of spore germination in the model bryophyte Physcomitrella patens (Aphanoregma patens). Our data suggest that the environmental signals regulating germination are conserved, but also that downstream hormone integration pathways mediating these responses in seeds were acquired after the evolution of the bryophyte lineage. Moreover, the role of abscisic acid and diterpenes (gibberellins) in germination assumed much greater importance as land plant evolution progressed. We conclude that the endogenous hormone signalling networks mediating germination in response to the environment may have evolved independently in spores and seeds. This paves the way for future research about how the mechanisms of plant dispersal on land evolved.
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Affiliation(s)
- Eleanor F. Vesty
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Younousse Saidi
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Laura A. Moody
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Daniel Holloway
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Amy Whitbread
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Sarah Needs
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Anushree Choudhary
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Bethany Burns
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Daniel McLeod
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Susan J. Bradshaw
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Hansol Bae
- Department of Systems BiologyTechnical University of DenmarkSøltofts Plads, 2800 KgsLyngbyDenmark
| | - Brian Christopher King
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
| | - George W. Bassel
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Henrik Toft Simonsen
- Department of Systems BiologyTechnical University of DenmarkSøltofts Plads, 2800 KgsLyngbyDenmark
| | - Juliet C. Coates
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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36
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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Inoue K, Nishihama R, Kataoka H, Hosaka M, Manabe R, Nomoto M, Tada Y, Ishizaki K, Kohchi T. Phytochrome Signaling Is Mediated by PHYTOCHROME INTERACTING FACTOR in the Liverwort Marchantia polymorpha. THE PLANT CELL 2016; 28:1406-21. [PMID: 27252292 PMCID: PMC4944405 DOI: 10.1105/tpc.15.01063] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 05/18/2016] [Accepted: 05/30/2016] [Indexed: 05/18/2023]
Abstract
Phytochromes are red light (R) and far-red light (FR) receptors that play important roles in many aspects of plant growth and development. Phytochromes mainly function in the nucleus and regulate sets of genes by inhibiting negatively acting basic helix-loop-helix transcription factors named PHYTOCHROME INTERACTING FACTORs (PIFs) in Arabidopsis thaliana Although R/FR photoreversible responses and phytochrome genes are well documented in diverse lineages of plants, the extent to which phytochrome signaling is mediated by gene regulation beyond angiosperms remains largely unclear. Here, we show that the liverwort Marchantia polymorpha, an emerging model basal land plant, has only one phytochrome gene, Mp-PHY, and only one PIF gene, Mp-PIF These genes mediate typical low fluence responses, which are reversibly elicited by R and FR, and regulate gene expression. Mp-phy is light-stable and translocates into the nucleus upon irradiation with either R or FR, demonstrating that the single phytochrome Mp-phy exhibits combined biochemical and cell-biological characteristics of type I and type II phytochromes. Mp-phy photoreversibly regulates gemma germination and downstream gene expression by interacting with Mp-PIF and targeting it for degradation in an R-dependent manner. Our findings suggest that the molecular mechanisms for light-dependent transcriptional regulation mediated by PIF transcription factors were established early in land plant evolution.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hideo Kataoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masashi Hosaka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryo Manabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Schuessele C, Hoernstein SNW, Mueller SJ, Rodriguez-Franco M, Lorenz T, Lang D, Igloi GL, Reski R. Spatio-temporal patterning of arginyl-tRNA protein transferase (ATE) contributes to gametophytic development in a moss. THE NEW PHYTOLOGIST 2016; 209:1014-1027. [PMID: 26428055 DOI: 10.1111/nph.13656] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/14/2015] [Indexed: 06/05/2023]
Abstract
The importance of the arginyl-tRNA protein transferase (ATE), the enzyme mediating post-translation arginylation of proteins in the N-end rule degradation (NERD) pathway of protein stability, was analysed in Physcomitrella patens and compared to its known functions in other eukaryotes. We characterize ATE:GUS reporter lines as well as ATE mutants in P. patens to study the impact and function of arginylation on moss development and physiology. ATE protein abundance is spatially and temporally regulated in P. patens by hormones and light and is highly abundant in meristematic cells. Further, the amount of ATE transcript is regulated during abscisic acid signalling and downstream of auxin signalling. Loss-of-function mutants exhibit defects at various levels, most severely in developing gametophores, in chloroplast starch accumulation and senescence. Thus, arginylation is necessary for moss gametophyte development, in contrast to the situation in flowering plants. Our analysis further substantiates the conservation of the N-end rule pathway components in land plants and highlights lineage-specific features. We introduce moss as a model system to characterize the role of the NERD pathway as an additional layer of complexity in eukaryotic development.
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Affiliation(s)
- Christian Schuessele
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Institute of Biology 3, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Institute of Biology 3, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Stefanie J Mueller
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Marta Rodriguez-Franco
- Cell Biology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Timo Lorenz
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Gabor L Igloi
- Institute of Biology 3, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- FRIAS - Freiburg Institute for Advanced Studies, University of Freiburg, 79104, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
- TIP - Trinational Institute for Plant Research, Upper Rhine Valley, 79104, Freiburg, Germany
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Abstract
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives. Phytochromes are red-light photoreceptors in plants that regulate key life cycle processes, yet their evolutionary origins are not well understood. Using transcriptomic and genomic data, Li et al. find that canonical plant phytochromes originated in a common ancestor of land plants and charophyte algae.
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40
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Klose C, Viczián A, Kircher S, Schäfer E, Nagy F. Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors. THE NEW PHYTOLOGIST 2015; 206:965-71. [PMID: 26042244 PMCID: PMC4406131 DOI: 10.1111/nph.13207] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/05/2014] [Indexed: 05/19/2023]
Abstract
The photoreceptors phytochromes monitor the red/far-red part of the spectrum, exist in the biologically active Pfr (far-red absorbing) or inactive Pr (red absorbing) forms, and function as red/far-red light-regulated molecular switches to modulate plant development and growth. Phytochromes are synthesized in the cytoplasm, and light induces translocation of the Pfr conformer into the nucleus. Nuclear import of phytochromes is a highly regulated process and is fine-tuned by the quality and quantity of light. It appears that phytochrome A (phyA) and phytochrome B (phyB) do not possess active endogenous nuclear import signals (NLSs), thus light-induced translocation of these photoreceptors into the nucleus requires direct protein–protein interactions with their NLS-containing signaling partners. Sub-cellular partitioning of the various phytochrome species is mediated by different molecular machineries. Translocation of phyA into the nucleus is promoted by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL), but the identity of nuclear transport facilitators mediating the import of phyB-E into the nucleus remains elusive. Phytochromes localized in the nucleus are associated with specific protein complexes, termed photobodies. The size and distribution of these structures are regulated by the intensity and duration of irradiation, and circumstantial evidence indicates that they are involved in fine-tuning phytochrome signaling.
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Affiliation(s)
- Cornelia Klose
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - András Viczián
- Institute of Plant Biology, Biological Research CentreTemesvári krt. 62, H-6726, Szeged, Hungary
| | - Stefan Kircher
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - Eberhard Schäfer
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research CentreTemesvári krt. 62, H-6726, Szeged, Hungary
- School of Biological Sciences, Institute of Molecular Plant Science, University of EdinburghEdinburgh, EH9 3JH, UK
- Author for correspondence: Ferenc Nagy Tel: +36 62599718
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Buchberger T, Lamparter T. Streptophyte phytochromes exhibit an N-terminus of cyanobacterial origin and a C-terminus of proteobacterial origin. BMC Res Notes 2015; 8:144. [PMID: 25886068 PMCID: PMC4422448 DOI: 10.1186/s13104-015-1082-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Prototypical phytochromes exhibit an N-terminal tridomain (PGP) consisting of PAS, GAF and PHY domains and a C-terminal histidine kinase (HK). Results The mode of evolution of streptophyte, fungal and diatom phytochromes from bacteria is analyzed using two programs for sequence alignment and six programs for tree construction. Our results suggest that Bacteroidetes present the most ancient types of phytochromes. We found many examples of lateral gene transfer and rearrangements of PGP and HK sequences. The PGP and HK of streptophyte phytochromes seem to have different origins. In the most likely scenario, PGP was inherited from cyanobacteria, whereas the C-terminal portion originated from a proteobacterial protein with multiple PAS domains and a C-terminal HK. The plant PhyA and PhyB lineages go back to an early gene duplication event before the diversification of streptophytes. Fungal and diatom PGPs could have a common prokaryotic origin within proteobacteria. Early gene duplication is also obvious in fungal phytochromes. Conclusions The dominant question of the origin of plant phytochromes is difficult to tackle because the patterns differ among phylogenetic trees. We could partially overcome this problem by combining several alignment and tree construction algorithms and comparing many trees. A rearrangement of PGP and HK can directly explain the insertion of the two PAS domains by which streptophyte phytochromes are distinguished from all other phytochromes. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1082-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thorsten Buchberger
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, Karlsruhe, D-76128, Germany.
| | - Tilman Lamparter
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, Karlsruhe, D-76128, Germany.
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Galvão VC, Fankhauser C. Sensing the light environment in plants: photoreceptors and early signaling steps. Curr Opin Neurobiol 2015; 34:46-53. [PMID: 25638281 DOI: 10.1016/j.conb.2015.01.013] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 01/15/2015] [Accepted: 01/17/2015] [Indexed: 01/22/2023]
Abstract
Plants must constantly adapt to a changing light environment in order to optimize energy conversion through the process of photosynthesis and to limit photodamage. In addition, plants use light cues for timing of key developmental transitions such as initiation of reproduction (transition to flowering). Plants are equipped with a battery of photoreceptors enabling them to sense a very broad light spectrum spanning from UV-B to far-red wavelength (280-750nm). In this review we briefly describe the different families of plant photosensory receptors and the mechanisms by which they transduce environmental information to influence numerous aspects of plant growth and development throughout their life cycle.
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Affiliation(s)
- Vinicius Costa Galvão
- Centre for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH 1015 Lausanne, Switzerland
| | - Christian Fankhauser
- Centre for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH 1015 Lausanne, Switzerland.
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43
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Bao L, Yamamoto KT, Fujita T. Phototropism in gametophytic shoots of the moss Physcomitrella patens. PLANT SIGNALING & BEHAVIOR 2015; 10:e1010900. [PMID: 25848889 PMCID: PMC4623243 DOI: 10.1080/15592324.2015.1010900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
Shoot phototropism enables plants to position their photosynthetic organs in favorable light conditions and thus benefits growth and metabolism in land plants. To understand the evolution of this response, we established an experimental system to study phototropism in gametophores of the moss Physcomitrella patens. The phototropic response of gametophores occurs slowly; a clear response takes place more than 24 hours after the onset of unilateral light irradiation, likely due to the slow growth rate of gametophores. We also found that red and far-red light can induce phototropism, with blue light being less effective. These results suggest that plants used a broad range of light wavelengths as phototropic signals during the early evolution of land plants.
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Affiliation(s)
- Liang Bao
- Biosystems Science Course; Graduate School of Life Science; Hokkaido University; Sapporo, Japan
| | - Kotaro T Yamamoto
- Department of Biological Sciences; Faculty of Science; Hokkaido University; Sapporo, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences; Faculty of Science; Hokkaido University; Sapporo, Japan
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44
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Sineshchekov V, Sudnitsin A, Ádám É, Schäfer E, Viczián A. phyA-GFP is spectroscopically and photochemically similar to phyA and comprises both its native types, phyA’ and phyA”. Photochem Photobiol Sci 2014; 13:1671-1679. [DOI: https:/doi.org/10.1039/c4pp00220b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/16/2014] [Indexed: 12/17/2023]
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45
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Sineshchekov V, Sudnitsin A, Ádám É, Schäfer E, Viczián A. phyA-GFP is spectroscopically and photochemically similar to phyA and comprises both its native types, phyA' and phyA''. Photochem Photobiol Sci 2014; 13:1671-9. [PMID: 25297540 DOI: 10.1039/c4pp00220b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/16/2014] [Indexed: 12/16/2023]
Abstract
Low-temperature fluorescence investigations of phyA-GFP used in experiments on its nuclear-cytoplasmic partitioning were carried out. In etiolated hypocotyls of phyA-deficient Arabidopsis thaliana expressing phyA-GFP, it was found that it is similar to phyA in spectroscopic parameters with both its native types, phyA' and phyA'', present and their ratio shifted towards phyA'. In transgenic tobacco hypocotyls, native phyA and rice phyA-GFP were also identical to phyA in the wild type whereas phyA-GFP belonged primarily to the phyA' type. Finally, truncated oat Δ6-12 phyA-GFP expressed in phyA-deficient Arabidopsis was represented by the phyA' type in contrast to full-length oat phyA-GFP with an approximately equal proportion of the two phyA types. This correlates with a previous observation that Δ6-12 phyA-GFP can form only numerous tiny subnuclear speckles while its wild-type counterpart can also localize into bigger and fewer subnuclear protein complexes. Thus, phyA-GFP is spectroscopically and photochemically similar or identical to the native phyA, suggesting that the GFP tag does not affect the chromophore. phyA-GFP comprises phyA'-GFP and phyA''-GFP, suggesting that both of them are potential participants in nuclear-cytoplasmic partitioning, which may contribute to its complexity.
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Affiliation(s)
- Vitaly Sineshchekov
- Biology Department, MV Lomonosov Moscow State University, Moscow 119899, Russia.
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46
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Marine algae and land plants share conserved phytochrome signaling systems. Proc Natl Acad Sci U S A 2014; 111:15827-32. [PMID: 25267653 DOI: 10.1073/pnas.1416751111] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte (<2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.
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47
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Ranjan A, Dickopf S, Ullrich KK, Rensing SA, Hoecker U. Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation. BMC PLANT BIOLOGY 2014; 14:178. [PMID: 24985152 PMCID: PMC4091655 DOI: 10.1186/1471-2229-14-178] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/24/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants have evolved light sensing mechanisms to optimally adapt their growth and development to the ambient light environment. The COP1/SPA complex is a key negative regulator of light signaling in the well-studied dicot Arabidopsis thaliana. COP1 and members of the four SPA proteins are part of an E3 ubiquitin ligase that acts in darkness to ubiquitinate several transcription factors involved in light responses, thereby targeting them for degradation by the proteasome. While COP1 is also found in humans, SPA proteins appear specific to plants. Here, we have functionally addressed evolutionary conservation of COP1 and SPA orthologs from the moss Physcomitrella, the monocot rice and the dicot Arabidopsis. RESULTS To this end, we analyzed the activities of COP1- and SPA-like proteins from Physcomitrella patens and rice when expressed in Arabidopsis. Expression of rice COP1 and Physcomitrella COP1 protein sequences predominantly complemented all phenotypic aspects of the viable, hypomorphic cop1-4 mutant and the null, seedling-lethal cop1-5 mutant of Arabidopsis: rice COP1 fully rescued the constitutive-photomorphogenesis phenotype in darkness and the leaf expansion defect of cop1 mutants, while it partially restored normal photoperiodic flowering in cop1. Physcomitrella COP1 partially restored normal seedling growth and flowering time, while it fully restored normal leaf expansion in the cop1 mutants. In contrast, expression of a SPA ortholog from Physcomitrella (PpSPAb) in Arabidopsis spa mutants did not rescue any facet of the spa mutant phenotype, suggesting that the PpSPAb protein is not functionally conserved or that the Arabidopsis function evolved after the split of mosses and seed plants. The SPA1 ortholog from rice (OsSPA1) rescued the spa mutant phenotype in dark-grown seedlings, but did not complement any spa mutant phenotype in light-grown seedlings or in adult plants. CONCLUSION Our results show that COP1 protein sequences from Physcomitrella, rice and Arabidopsis have been functionally conserved during evolution, while the SPA proteins showed considerable functional divergence. This may - at least in part - reflect the fact that COP1 is a single copy gene in seed plants, while SPA proteins are encoded by a small gene family of two to four members with possibly sub- or neofunctionalized tasks.
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Affiliation(s)
- Aashish Ranjan
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
- Present addresss: Life Sciences Addition #2237, Section of Plant Biology, UC Davis, One Shields Ave, Davis, CA 95616, USA
| | - Stephen Dickopf
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
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Casal JJ, Candia AN, Sellaro R. Light perception and signalling by phytochrome A. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2835-45. [PMID: 24220656 DOI: 10.1093/jxb/ert379] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In etiolated seedlings, phytochrome A (phyA) mediates very-low-fluence responses (VLFRs), which initiate de-etiolation at the interphase between the soil and above-ground environments, and high-irradiance responses (HIR), which complete de-etiolation under dense canopies and require more sustained activation with far-red light. Light-activated phyA is transported to the nucleus by FAR-RED ELONGATED HYPOCOTYL1 (FHY1). The nuclear pool of active phyA increases under prolonged far-red light of relatively high fluence rates. This condition maximizes the rate of FHY1-phyA complex assembly and disassembly, allowing FHY1 to return to the cytoplasm to translocate further phyA to the nucleus, to replace phyA degraded in the proteasome. The core signalling pathways downstream of nuclear phyA involve the negative regulation of CONSTITUTIVE PHOTOMORPHOGENIC 1, which targets for degradation transcription factors required for photomorphogenesis, and PHYTOCHROME-INTERACTING FACTORs, which are transcription factors that repress photomorphogenesis. Under sustained far-red light activation, released FHY1 can also be recruited with active phyA to target gene promoters as a transcriptional activator, and nuclear phyA signalling activates a positive regulatory loop involving BELL-LIKE HOMEODOMAIN 1 that reinforces the HIR.
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Affiliation(s)
- J J Casal
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and CONICET, 1417 Buenos Aires, Argentina Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, C1405BWE Buenos Aires, Argentina
| | - A N Candia
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and CONICET, 1417 Buenos Aires, Argentina
| | - R Sellaro
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and CONICET, 1417 Buenos Aires, Argentina
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Possart A, Fleck C, Hiltbrunner A. Shedding (far-red) light on phytochrome mechanisms and responses in land plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 217-218:36-46. [PMID: 24467894 DOI: 10.1016/j.plantsci.2013.11.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 05/20/2023]
Abstract
In order to monitor ambient light conditions, plants rely on functionally diversified photoreceptors. Among these, phytochromes perceive red (R) and far-red (FR) light. FR light does not constitute a photosynthetic energy source; it however influences adaptive and developmental processes. In seed plants, phytochrome A (phyA) acts as FR receptor and mediates FR high irradiance responses (FR-HIRs). It exerts a dual role by promoting e.g. germination and seedling de-etiolation in canopy shade and by antagonising shade avoidance growth. Even though cryptogam plants such as mosses and ferns do not have phyA, they show FR-induced responses. In the present review we discuss the mechanistic basis of phyA-dependent FR-HIRs as well as their dual role in seed plants. We compare FR responses in seed plants and cryptogam plants and conclude on different potential concepts for the detection of canopy shade. Scenarios for the evolution of FR perception and responses are discussed.
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Affiliation(s)
- Anja Possart
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christian Fleck
- Laboratory for Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands.
| | - Andreas Hiltbrunner
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Wu HP, Su YS, Chen HC, Chen YR, Wu CC, Lin WD, Tu SL. Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol 2014; 15:R10. [PMID: 24398233 PMCID: PMC4054894 DOI: 10.1186/gb-2014-15-1-r10] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/07/2014] [Indexed: 12/22/2022] Open
Abstract
Background Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of gene expression are modulated by photoreceptors, regulation at the mRNA splicing step remains unclear. Results We performed high-throughput mRNA sequencing to analyze light-responsive changes in alternative splicing in the moss Physcomitrella patens, and found that a large number of alternative splicing events were induced by light in the moss protonema. Light-responsive intron retention preferentially occurred in transcripts involved in photosynthesis and translation. Many of the alternatively spliced transcripts were expressed from genes with a function relating to splicing or light signaling, suggesting a potential impact on pre-mRNA splicing and photomorphogenic gene regulation in response to light. Moreover, most light-regulated intron retention was induced immediately upon light exposure, while motif analysis identified a repetitive GAA motif that may function as an exonic regulatory cis element in light-mediated alternative splicing. Further analysis in gene-disrupted mutants was consistent with a function for multiple red-light photoreceptors in the upstream regulation of light-responsive alternative splicing. Conclusions Our results indicate that intensive alternative splicing occurs in non-vascular plants and that, during photomorphogenesis, light regulates alternative splicing with transcript selectivity. We further suggest that alternative splicing is rapidly fine-tuned by light to modulate gene expression and reorganize metabolic processes, and that pre-mRNA cis elements are involved in photoreceptor-mediated splicing regulation.
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