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Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H, Deng XW. Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings. NATURE PLANTS 2023; 9:2095-2109. [PMID: 37903986 PMCID: PMC10724060 DOI: 10.1038/s41477-023-01544-4] [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: 10/10/2022] [Accepted: 09/19/2023] [Indexed: 11/01/2023]
Abstract
Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.
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Affiliation(s)
- Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zhiying Lou
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Zheng Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Chunlei Gao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yi Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zizheng Ren
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Weimin Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Wenbo Pan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Huawei Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Qing Sang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Miaomiao Wan
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
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Liu Y, Wang Q, Abbas F, Zhou Y, He J, Fan Y, Yu R. Light Regulation of LoCOP1 and Its Role in Floral Scent Biosynthesis in Lilium 'Siberia'. PLANTS (BASEL, SWITZERLAND) 2023; 12:2004. [PMID: 37653921 PMCID: PMC10223427 DOI: 10.3390/plants12102004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 09/02/2023]
Abstract
Light is an important environmental signal that governs plant growth, development, and metabolism. Constitutive photomorphogenic 1 (COP1) is a light signaling component that plays a vital role in plant light responses. We isolated the COP1 gene (LoCOP1) from the petals of Lilium 'Siberia' and investigated its function. The LoCOP1 protein was found to be the most similar to Apostasia shenzhenica COP1. LoCOP1 was found to be an important factor located in the nucleus and played a negative regulatory role in floral scent production and emission using the virus-induced gene silencing (VIGS) approach. The yeast two-hybrid, β-galactosidase, and bimolecular fluorescence complementation (BiFC) assays revealed that LoCOP1 interacts with LoMYB1 and LoMYB3. Furthermore, light modified both the subcellular distribution of LoCOP1 and its interactions with LoMYB1 and MYB3 in onion cells. The findings highlighted an important regulatory mechanism in the light signaling system that governs scent emission in Lilium 'Siberia' by the ubiquitination and degradation of transcription factors via the proteasome pathway.
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Affiliation(s)
- Yang Liu
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Q.W.); (F.A.); (Y.Z.); (J.H.)
| | - Qin Wang
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Q.W.); (F.A.); (Y.Z.); (J.H.)
| | - Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Q.W.); (F.A.); (Y.Z.); (J.H.)
| | - Yiwei Zhou
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Q.W.); (F.A.); (Y.Z.); (J.H.)
| | - Jingjuan He
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Q.W.); (F.A.); (Y.Z.); (J.H.)
| | - Yanping Fan
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Q.W.); (F.A.); (Y.Z.); (J.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Rangcai Yu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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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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Zhang Y, Zhou J, Zhang Y, Zhang D. The ABI3 Transcription Factor Interaction and Antagonism with Ubiquitin E3 Ligase ScPRT1 in Syntrichia caninervis. Genes (Basel) 2022; 13:genes13050718. [PMID: 35627103 PMCID: PMC9141515 DOI: 10.3390/genes13050718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 02/05/2023] Open
Abstract
The ubiquitination pathway has been found to regulate plant responses to environmental stress. However, the role of E3 ubiquitin ligase in desiccation tolerant moss has not yet been elucidated. Previous research has shown that the abscisic acid (ABA) signaling factor ScABI3 can significantly increase desiccation tolerance and reduce ABA sensitivity in the desert moss Syntrichia caninervis. In this study, we identified a RING-type E3 ubiquitin ligase, ScPRT1, and showed that ScABI3 can directly interact with ScPRT1 in vitro and in vivo. Furthermore, we found that the high expression of ScPRT1 can interfere with the transcription of ScABI3 under ABA treatment. Therefore, we speculate that ScPRT1 may degrade ScABI3 through the ubiquitin-26S proteasome system and participate in ABA-dependent signaling in response to ABA-insensitivity or desiccation tolerance in S. caninervis. The findings from our study may enrich our knowledge of the role of E3 ubiquitin ligase in desiccation tolerance and lay a theoretical foundation for an in-depth study of the relationship between ubiquitination modification and ABA signal transduction under environmental stress.
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Affiliation(s)
- Yigong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Y.Z.); (J.Z.); (Y.Z.)
| | - Jiyang Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Y.Z.); (J.Z.); (Y.Z.)
| | - Yi Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Y.Z.); (J.Z.); (Y.Z.)
| | - Daoyuan Zhang
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838099, China
- Correspondence:
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Zhang L, Li T, Su S, Peng H, Li S, Li K, Ji L, Xing Y, Zhang J, Du X, Bian M, Liao Y, Yang Z, Zuo Z. Functions of COP1/SPA E3 Ubiquitin Ligase Mediated by MpCRY in the Liverwort Marchantia polymorpha under Blue Light. Int J Mol Sci 2021; 23:ijms23010158. [PMID: 35008588 PMCID: PMC8745113 DOI: 10.3390/ijms23010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 12/03/2022] Open
Abstract
COP1/SPA1 complex in Arabidopsis inhibits photomorphogenesis through the ubiquitination of multiple photo-responsive transcription factors in darkness, but such inhibiting function of COP1/SPA1 complex would be suppressed by cryptochromes in blue light. Extensive studies have been conducted on these mechanisms in Arabidopsis whereas little attention has been focused on whether another branch of land plants bryophyte utilizes this blue-light regulatory pathway. To study this problem, we conducted a study in the liverwort Marchantia polymorpha and obtained a MpSPA knock-out mutant, in which Mpspa exhibits the phenotype of an increased percentage of individuals with asymmetrical thallus growth, similar to MpCRY knock-out mutant. We also verified interactions of MpSPA with MpCRY (in a blue light-independent way) and with MpCOP1. Concomitantly, both MpSPA and MpCOP1 could interact with MpHY5, and MpSPA can promote MpCOP1 to ubiquitinate MpHY5 but MpCRY does not regulate the ubiquitination of MpHY5 by MpCOP1/MpSPA complex. These data suggest that COP1/SPA ubiquitinating HY5 is conserved in Marchantia polymorpha, but dissimilar to CRY in Arabidopsis, MpCRY is not an inhibitor of this process under blue light.
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Affiliation(s)
- Li Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Tianhong Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Shengzhong Su
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Hao Peng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530001, China; (H.P.); (Y.L.)
| | - Sudi Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Ke Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (L.J.); (Y.X.)
| | - Luyao Ji
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (L.J.); (Y.X.)
| | - Yaoyun Xing
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (L.J.); (Y.X.)
| | - Junchuan Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
| | - Yuying Liao
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530001, China; (H.P.); (Y.L.)
| | - Zhenming Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
- Correspondence: (Z.Y.); (Z.Z.)
| | - Zecheng Zuo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Z.); (T.L.); (S.S.); (S.L.); (J.Z.); (X.D.); (M.B.)
- Correspondence: (Z.Y.); (Z.Z.)
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Kang CH, Lee ES, Nawkar GM, Park JH, Wi SD, Bae SB, Chae HB, Paeng SK, Hong JC, Lee SY. Constitutive Photomorphogenic 1 Enhances ER Stress Tolerance in Arabidopsis. Int J Mol Sci 2021; 22:ijms221910772. [PMID: 34639112 PMCID: PMC8509555 DOI: 10.3390/ijms221910772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/26/2022] Open
Abstract
Interaction between light signaling and stress response has been recently reported in plants. Here, we investigated the role of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a key regulator of light signaling, in endoplasmic reticulum (ER) stress response in Arabidopsis. The cop1-4 mutant Arabidopsis plants were highly sensitive to ER stress induced by treatment with tunicarmycin (Tm). Interestingly, the abundance of nuclear-localized COP1 increased under ER stress conditions. Complementation of cop1-4 mutant plants with the wild-type or variant types of COP1 revealed that the nuclear localization and dimerization of COP1 are essential for its function in plant ER stress response. Moreover, the protein amount of ELONGATED HYPOCOTYL 5 (HY5), which inhibits bZIP28 to activate the unfolded protein response (UPR), decreased under ER stress conditions in a COP1-dependent manner. Accordingly, the binding of bZIP28 to the BIP3 promoter was reduced in cop1-4 plants and increased in hy5 plants compared with the wild type. Furthermore, introduction of the hy5 mutant locus into the cop1-4 mutant background rescued its ER stress-sensitive phenotype. Altogether, our results suggest that COP1, a negative regulator of light signaling, positively controls ER stress response by partially degrading HY5 in the nucleus.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jong Chan Hong
- Correspondence: (J.C.H.); (S.Y.L.); Tel.: +82-55-772-1353 (J.C.H.); +82-55-772-1351 (S.Y.L.); Fax: +82-55-759-9363
| | - Sang Yeol Lee
- Correspondence: (J.C.H.); (S.Y.L.); Tel.: +82-55-772-1353 (J.C.H.); +82-55-772-1351 (S.Y.L.); Fax: +82-55-759-9363
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Kim B, Piao R, Lee G, Koh E, Lee Y, Woo S, Jiang W, Septiningsih EM, Thomson MJ, Koh HJ. OsCOP1 regulates embryo development and flavonoid biosynthesis in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2587-2601. [PMID: 33950284 PMCID: PMC8277627 DOI: 10.1007/s00122-021-03844-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/22/2021] [Indexed: 06/07/2023]
Abstract
Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds.
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Affiliation(s)
- Backki Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Rihua Piao
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, 136100 China
| | - Gileung Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Eunbyeol Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 08826 Republic of Korea
| | - Wenzhu Jiang
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062 China
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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Aratboni HA, Rafiei N, Khorashad LK, Lerma-Escalera AI, Balderas-Cisneros FDJ, Liu Z, Alemzadeh A, Shaji S, Morones-Ramírez JR. LED control of gene expression in a nanobiosystem composed of metallic nanoparticles and a genetically modified E. coli strain. J Nanobiotechnology 2021; 19:190. [PMID: 34174890 PMCID: PMC8236197 DOI: 10.1186/s12951-021-00937-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Within the last decade, genetic engineering and synthetic biology have revolutionized society´s ability to mass-produce complex biological products within genetically-modified microorganisms containing elegantly designed genetic circuitry. However, many challenges still exist in developing bioproduction processes involving genetically modified microorganisms with complex or multiple gene circuits. These challenges include the development of external gene expression regulation methods with the following characteristics: spatial-temporal control and scalability, while inducing minimal permanent or irreversible system-wide conditions. Different stimuli have been used to control gene expression and mitigate these challenges, and they can be characterized by the effect they produce in the culture media conditions. Invasive stimuli that cause permanent, irreversible changes (pH and chemical inducers), non-invasive stimuli that cause partially reversible changes (temperature), and non-invasive stimuli that cause reversible changes in the media conditions (ultrasound, magnetic fields, and light). METHODS Opto-control of gene expression is a non-invasive external trigger that complies with most of the desired characteristics of an external control system. However, the disadvantage relies on the design of the biological photoreceptors and the necessity to design them to respond to a different wavelength for every bioprocess needed to be controlled or regulated in the microorganism. Therefore, this work proposes using biocompatible metallic nanoparticles as external controllers of gene expression, based on their ability to convert light into heat and the capacity of nanotechnology to easily design a wide array of nanostructures capable of absorbing light at different wavelengths and inducing plasmonic photothermal heating. RESULTS Here, we designed a nanobiosystem that can be opto-thermally triggered using LED light. The nanobiosystem is composed of biocompatible gold nanoparticles and a genetically modified E. coli with a plasmid that allows mCherry fluorescent protein production at 37 °C in response to an RNA thermometer. CONCLUSIONS The LED-triggered photothermal protein production system here designed offers a new, cheaper, scalable switchable method, non-destructive for living organisms, and contribute toward the evolution of bioprocess production systems.
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Affiliation(s)
- Hossein Alishah Aratboni
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas, Av. Universidad s/n. CD. Universitaria, San Nicolás de los Garza, 66451, Nuevo León, México
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México
| | - Nahid Rafiei
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas, Av. Universidad s/n. CD. Universitaria, San Nicolás de los Garza, 66451, Nuevo León, México
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Km. 12 Shiraz-Isfahan highway, Bajgah area, 71441-65186, Shiraz, Iran
| | - Larousse Khosravi Khorashad
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Albert Isaac Lerma-Escalera
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas, Av. Universidad s/n. CD. Universitaria, San Nicolás de los Garza, 66451, Nuevo León, México
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México
| | - Francisco de Jesús Balderas-Cisneros
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas, Av. Universidad s/n. CD. Universitaria, San Nicolás de los Garza, 66451, Nuevo León, México
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México
| | - Zhaowei Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Abbas Alemzadeh
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Km. 12 Shiraz-Isfahan highway, Bajgah area, 71441-65186, Shiraz, Iran.
| | - Sadasivan Shaji
- Universidad Autónoma de Nuevo León, UANL. Facultad de ingeniería mecánica y eléctrica, Universidad s/n. CD. Universitaria, 66451, Nuevo León, San Nicolás de los Garza, México
| | - José Ruben Morones-Ramírez
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas, Av. Universidad s/n. CD. Universitaria, San Nicolás de los Garza, 66451, Nuevo León, México.
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México.
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9
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Cao S, Luo X, Xu D, Tian X, Song J, Xia X, Chu C, He Z. Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals. THE NEW PHYTOLOGIST 2021; 230:1731-1745. [PMID: 33586137 DOI: 10.1111/nph.17276] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 05/23/2023]
Abstract
Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuling Tian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China
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10
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Xu C, Chang X, Hou Z, Zhang Z, Zhu Z, Zhong B. The origin of SPA reveals the divergence and convergence of light signaling in Archaeplastida. Mol Phylogenet Evol 2021; 161:107175. [PMID: 33862251 DOI: 10.1016/j.ympev.2021.107175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
Plants have evolved various photoreceptors to adapt to changing light environments, and photoreceptors can inactivate the large CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETIOLATED/FUSCA (COP/DET/FUS) protein complex to release their repression of photoresponsive transcription factors. Here, we tracked the origin and evolution of COP/DET/FUS in Archaeplastida and found that most components of COP/DET/FUS were highly conserved. Intriguingly, the COP1-SUPPRESSOR OF PHYA-105 (SPA) protein originated in Chlorophyta but subsequently underwent a distinct evolutionary history in Viridiplantae. SPA experienced duplication events in the ancestors of specific clades after the colonization of land by plants and was divided into two clades (clades A and B) within euphyllophytes (ferns and seed plants). Our phylogenetic and experimental evidences support a new evolutionary model to clarify the divergence and convergence of light signaling during plant evolution.
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Affiliation(s)
- Chenjie Xu
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China
| | - Zheng Hou
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China
| | - Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China.
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11
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Phokas A, Coates JC. Evolution of DELLA function and signaling in land plants. Evol Dev 2021; 23:137-154. [PMID: 33428269 PMCID: PMC9285615 DOI: 10.1111/ede.12365] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/21/2020] [Accepted: 11/28/2020] [Indexed: 01/08/2023]
Abstract
DELLA proteins are master growth regulators that repress responses to a group of plant growth hormones called gibberellins (GAs). Manipulation of DELLA function and signaling was instrumental in the development of high‐yielding crop varieties that saved millions from starvation during the “Green Revolution.” Despite decades of extensive research, it is still unclear how DELLA function and signaling mechanisms evolved within the land plant lineage. Here, we review current knowledge on DELLA protein function with reference to structure, posttranslational modifications, downstream transcriptional targets, and protein–protein interactions. Furthermore, we discuss older and recent findings regarding the evolution of DELLA signaling within the land plant lineage, with an emphasis on bryophytes, and identify future avenues of research that would enable us to shed more light on the evolution of DELLA signaling. Unraveling how DELLA function and signaling mechanisms have evolved could enable us to engineer better crops in an attempt to contribute to mitigating the effects of global warming and achieving global food security. DELLA genes first appeared in the common ancestor of land plants and underwent two major duplications during land plant evolution. DELLAs repress gibberellin responses in vascular plants but their function in nonvascular plants remains elusive.
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Affiliation(s)
- Alexandros Phokas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
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12
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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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13
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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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14
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Han X, Huang X, Deng XW. The Photomorphogenic Central Repressor COP1: Conservation and Functional Diversification during Evolution. PLANT COMMUNICATIONS 2020; 1:100044. [PMID: 33367240 PMCID: PMC7748024 DOI: 10.1016/j.xplc.2020.100044] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/19/2020] [Accepted: 04/07/2020] [Indexed: 05/23/2023]
Abstract
Green plants on the earth have evolved intricate mechanisms to acclimatize to and utilize sunlight. In Arabidopsis, light signals are perceived by photoreceptors and transmitted through divergent but overlapping signaling networks to modulate plant photomorphogenic development. COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) was first cloned as a central repressor of photomorphogenesis in higher plants and has been extensively studied for over 30 years. It acts as a RING E3 ubiquitin ligase downstream of multiple photoreceptors to target key light-signaling regulators for degradation, primarily as part of large protein complexes. The mammalian counterpart of COP1 is a pluripotent regulator of tumorigenesis and metabolism. A great deal of information on COP1 has been derived from whole-genome sequencing and functional studies in lower green plants, which enables us to illustrate its evolutionary history. Here, we review the current understanding about COP1, with a focus on the conservation and functional diversification of COP1 and its signaling partners in different taxonomic clades.
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Affiliation(s)
- Xue Han
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University-Southern University of Science and Technology Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University-Southern University of Science and Technology Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
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15
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Wei H, Kong D, Yang J, Wang H. Light Regulation of Stomatal Development and Patterning: Shifting the Paradigm from Arabidopsis to Grasses. PLANT COMMUNICATIONS 2020; 1:100030. [PMID: 33367232 PMCID: PMC7747992 DOI: 10.1016/j.xplc.2020.100030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/30/2019] [Accepted: 02/06/2020] [Indexed: 05/22/2023]
Abstract
The stomatal pores of plant leaves control gas exchange with the environment. Stomatal development is prevised regulated by both internal genetic programs and environmental cues. Among various environmental factors, light regulation of stomata formation has been extensively studied in Arabidopsis. In this review, we summarize recent advances in the genetic control of stomata development and its regulation by light. We also present a comparative analysis of the conserved and diverged stomatal regulatory networks between Arabidopsis and cereal grasses. Lastly, we provide our perspectives on manipulation of the stomata density on plant leaves for the purpose of breeding crops that are better adapted to the adverse environment and high-density planting conditions.
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Affiliation(s)
- Hongbin Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Juan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Corresponding author
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16
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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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17
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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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18
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Hiltbrunner A. Shedding light on the evolution of light signalling. THE NEW PHYTOLOGIST 2019; 224:1412-1414. [PMID: 31587283 DOI: 10.1111/nph.16175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
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19
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Carbonare LD, White MD, Shukla V, Francini A, Perata P, Flashman E, Sebastiani L, Licausi F. Zinc Excess Induces a Hypoxia-Like Response by Inhibiting Cysteine Oxidases in Poplar Roots. PLANT PHYSIOLOGY 2019; 180:1614-1628. [PMID: 31019003 PMCID: PMC6752924 DOI: 10.1104/pp.18.01458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/12/2019] [Indexed: 05/24/2023]
Abstract
Poplar (Populus spp.) is a tree species considered for the remediation of soil contaminated by metals, including zinc (Zn). To improve poplar's capacity for Zn assimilation and compartmentalization, it is necessary to understand the physiological and biochemical mechanisms that enable these features as well as their regulation at the molecular level. We observed that the molecular response of poplar roots to Zn excess overlapped with that activated by hypoxia. Therefore, we tested the effect of Zn excess on hypoxia-sensing components and investigated the consequence of root hypoxia on poplar fitness and Zn accumulation capacity. Our results suggest that high intracellular Zn concentrations mimic iron deficiency and inhibit the activity of the oxygen sensors Plant Cysteine Oxidases, leading to the stabilization and activation of ERF-VII transcription factors, which are key regulators of the molecular response to hypoxia. Remarkably, excess Zn and waterlogging similarly decreased poplar growth and development. Simultaneous excess Zn and waterlogging did not exacerbate these parameters, although Zn uptake was limited. This study unveils the contribution of the oxygen-sensing machinery to the Zn excess response in poplar, which may be exploited to improve Zn tolerance and increase Zn accumulation capacity in plants.
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Affiliation(s)
| | - Mark D White
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Vinay Shukla
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Alessandra Francini
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Emily Flashman
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Luca Sebastiani
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Francesco Licausi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
- Biology Department, University of Pisa, 56126 Pisa, Italy
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20
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Han X, Chang X, Zhang Z, Chen H, He H, Zhong B, Deng XW. Origin and Evolution of Core Components Responsible for Monitoring Light Environment Changes during Plant Terrestrialization. MOLECULAR PLANT 2019; 12:847-862. [PMID: 31009752 DOI: 10.1016/j.molp.2019.04.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 05/22/2023]
Abstract
Light serves as the source of energy as well as an information signal for photosynthetic plants. During evolution, plants have acquired the ability to monitor environmental light radiation and adjust their developmental patterns to optimally utilize light energy for photosynthesis. The mechanisms of light perception and signal transduction have been comprehensively studied in past decades, mostly in a few model plants, including Arabidopsis thaliana. However, systematic analyses of the origin and evolution of core components involved in light perception and signaling are still lacking. In this study, we took advantage of the recently sequenced genomes and transcriptomes covering all the main Archaeplastida clades in the public domain to identify orthologous genes of core components involved in light perception and signaling and to reconstruct their evolutionary history. Our analyses suggested that acclimation to different distribution of light quality in new environments led to the origination of specific light signaling pathways in plants. The UVR8 (UV Resistance Locus 8) signaling pathway originated during the movement of plants from the deeper sea to shallow water and enabled plants to deal with ultraviolet B light (UV-B). After acquisition of UV-B adaptation, origination of the phytochrome signaling pathway helped plants to colonize water surface where red light became the prominent light energy source. The seedling emergence pathway, which is mediated by a combination of light and phytohormone signals that orchestrate plant growth pattern transitions, originated before the emergence of seed plants. Although cryptochromes and some key components of E3 ubiquitin ligase systems already existed before the divergence of the plant and animal kingdoms, the coevolution and optimization of light perception and downstream signal transduction components, including key transcription factors and E3 ubiquitin ligase systems, are evident during plant terrestrialization.
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Affiliation(s)
- Xue Han
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Haodong Chen
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China.
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
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21
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Podolec R, Ulm R. Photoreceptor-mediated regulation of the COP1/SPA E3 ubiquitin ligase. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:18-25. [PMID: 29775763 DOI: 10.1016/j.pbi.2018.04.018] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/25/2018] [Accepted: 04/29/2018] [Indexed: 05/19/2023]
Abstract
Plants have evolved specific photoreceptors that capture informational cues from sunlight. The phytochrome, cryptochrome, and UVR8 photoreceptors perceive red/far-red, blue/UV-A, and UV-B light, respectively, and control overlapping photomorphogenic responses important for plant growth and development. A major repressor of such photomorphogenic responses is the E3 ubiquitin ligase formed by CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) proteins, which acts by regulating the stability of photomorphogenesis-promoting transcription factors. The direct interaction of light-activated photoreceptors with the COP1/SPA complex represses its activity via nuclear exclusion of COP1, disruption of the COP1-SPA interaction, and/or SPA protein degradation. This process enables plants to integrate different light signals at the level of the COP1/SPA complex to enact appropriate photomorphogenic responses according to the light environment.
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Affiliation(s)
- Roman Podolec
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Roman Ulm
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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22
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Jiménez-López D, Muñóz-Belman F, González-Prieto JM, Aguilar-Hernández V, Guzmán P. Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes. PLoS One 2018; 13:e0203442. [PMID: 30169501 PMCID: PMC6118397 DOI: 10.1371/journal.pone.0203442] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/21/2018] [Indexed: 01/12/2023] Open
Abstract
E3 ubiquitin ligases of the ubiquitin proteasome system (UPS) mediate recognition of substrates and later transfer the ubiquitin (Ub). They are the most expanded components of the system. The Really Interesting New Gene (RING) domain contains 40-60 residues that are highly represented among E3 ubiquitin ligases. The Arabidopsis thaliana E3 ubiquitin ligases with a RING finger primarily contain RING-HC or RING-H2 type domains or less frequently RING-v, RING-C2, RING-D, RING-S/T and RING-G type domains. Our previous work on three E3 ubiquitin ligase families with a RING-H2 type domain, ATL, BTL, and CTL, suggested that a phylogenetic distribution based on the RING domain allowed for the creation a catalog of known domains or unknown conserved motifs. This work provided a useful and comprehensive view of particular families of RING E3 ubiquitin ligases. We updated the annotation of A. thaliana RING proteins and surveyed RING proteins from 30 species across eukaryotes. Based on domain architecture profile of the A. thaliana proteins, we catalogued 4711 RING finger proteins into 107 groups, including 66 previously described gene families or single genes and 36 novel families or undescribed genes. Forty-four groups were specific to a plant lineage while 41 groups consisted of proteins found in all eukaryotic species. Our present study updates the current classification of plant RING finger proteins and reiterates the importance of these proteins in plant growth and adaptation.
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Affiliation(s)
- Domingo Jiménez-López
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Gto., México
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Francisco Muñóz-Belman
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Gto., México
| | - Juan Manuel González-Prieto
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Victor Aguilar-Hernández
- CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Col. Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Gto., México
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23
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Abstract
500Ma ago the terrestrial habitat was a barren, unwelcoming place for species other than, for example, bacteria or fungi. Most probably, filamentous freshwater algae adapted to aerial conditions and eventually conquered land. Adaptation to a severely different habitat apparently included sturdy cell walls enabling an erect body plan as well as protection against abiotic stresses such as ultraviolet radiation, drought and varying temperature. To thrive on land, plants probably required more elaborate signaling pathways to react to diverse environmental conditions, and phytohormones to control developmental programs. Many such plant-typical features have been studied in flowering plants, but their evolutionary origins were long clouded. With the sequencing of a moss genome a decade ago, inference of ancestral land plant states using comparative genomics, phylogenomics and evolutionary developmental approaches began in earnest. In the past few years, the ever increasing availability of genomic and transcriptomic data of organisms representing the earliest common ancestors of the plant tree of life has much informed our understanding of the conquest of land by plants.
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Affiliation(s)
- Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany.
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24
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Tevatia R, Oyler GA. Evolution of DDB1-binding WD40 (DWD) in the viridiplantae. PLoS One 2018; 13:e0190282. [PMID: 29293590 PMCID: PMC5749748 DOI: 10.1371/journal.pone.0190282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/11/2017] [Indexed: 12/16/2022] Open
Abstract
Damaged DNA Binding 1 (DDB1)—binding WD40 (DWD) proteins are highly conserved and involved in a plethora of developmental and physiological processes such as flowering time control, photomorphogenesis, and abiotic stress responses. The phylogeny of this family of proteins in plants and algae of viridiplante is a critical area to understand the emergence of this family in such important and diverse functions. We aimed to investigate the putative homologs of DWD in the viridiplante and establish a deeper DWD evolutionary grasp. The advancement in publicly available genomic data allowed us to perform an extensive genome-wide DWD retrieval. Using annotated Arabidopsis thaliana DWDs as the reference, we generated and characterized a comprehensive DWD database for the studied photoautotrophs. Further, a generic DWD classification system (Type A to K), based on (i) position of DWD motifs, (ii) number of DWD motifs, and (iii) presence/absence of other domains, was adopted. About 72–80% DWDs have one DWD motif, whereas 17–24% DWDs have two and 0.5–4.7% DWDs have three DWD motifs. Neighbor-joining phylogenetic construction of A. thaliana DWDs facilitated us to tune these substrate receptors into 15 groups. Though the DWD count increases from microalgae to higher land plants, the ratio of DWD to WD40 remained constant throughout the viridiplante. The DWD expansion appeared to be the consequence of consistent DWD genetic flow accompanied by several gene duplication events. The network, phylogenetic, and statistical analysis delineated DWD evolutionary relevance in the viridiplante.
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Affiliation(s)
- Rahul Tevatia
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (RT); (GAO)
| | - George A. Oyler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Synaptic Research LLC, Baltimore, Maryland, United States of America
- * E-mail: (RT); (GAO)
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25
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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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26
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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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27
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Frangedakis E, Saint‐Marcoux D, Moody LA, Rabbinowitsch E, Langdale JA. Nonreciprocal complementation of KNOX gene function in land plants. THE NEW PHYTOLOGIST 2017; 216:591-604. [PMID: 27886385 PMCID: PMC5637896 DOI: 10.1111/nph.14318] [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: 08/06/2016] [Accepted: 09/30/2016] [Indexed: 05/02/2023]
Abstract
Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins regulate development of the multicellular diploid sporophyte in both mosses and flowering plants; however, the morphological context in which they function differs. In order to determine how Class I KNOX function was modified as land plants evolved, phylogenetic analyses and cross-species complementation assays were performed. Our data reveal that a duplication within the charophyte sister group to land plants led to distinct Class I and Class II KNOX gene families. Subsequently, Class I sequences diverged substantially in the nonvascular bryophyte groups (liverworts, mosses and hornworts), with moss sequences being most similar to those in vascular plants. Despite this similarity, moss mutants were not complemented by vascular plant KNOX genes. Conversely, the Arabidopsis brevipedicellus (bp-9) mutant was complemented by the PpMKN2 gene from the moss Physcomitrella patens. Lycophyte KNOX genes also complemented bp-9 whereas fern genes only partially complemented the mutant. This lycophyte/fern distinction is mirrored in the phylogeny of KNOX-interacting BELL proteins, in that a gene duplication occurred after divergence of the two groups. Together, our results imply that the moss MKN2 protein can function in a broader developmental context than vascular plant KNOX proteins, the narrower scope having evolved progressively as lycophytes, ferns and flowering plants diverged.
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Affiliation(s)
| | - Denis Saint‐Marcoux
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Laura A. Moody
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Ester Rabbinowitsch
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Jane A. Langdale
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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28
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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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29
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Yang Z, Liu B, Su J, Liao J, Lin C, Oka Y. Cryptochromes Orchestrate Transcription Regulation of Diverse Blue Light Responses in Plants. Photochem Photobiol 2017; 93:112-127. [PMID: 27861972 DOI: 10.1111/php.12663] [Citation(s) in RCA: 290] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/02/2016] [Indexed: 11/30/2022]
Abstract
Blue light affects many aspects of plant growth and development throughout the plant lifecycle. Plant cryptochromes (CRYs) are UV-A/blue light photoreceptors that play pivotal roles in regulating blue light-mediated physiological responses via the regulated expression of more than one thousand genes. Photoactivated CRYs regulate transcription via two distinct mechanisms: indirect promotion of the activity of transcription factors by inactivation of the COP1/SPA E3 ligase complex or direct activation or inactivation of at least two sets of basic helix-loop-helix transcription factor families by physical interaction. Hence, CRYs govern intricate mechanisms that modulate activities of transcription factors to regulate multiple aspects of blue light-responsive photomorphogenesis. Here, we review recent progress in dissecting the pathways of CRY signaling and discuss accumulating evidence that shows how CRYs regulate broad physiological responses to blue light.
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Affiliation(s)
- Zhaohe Yang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bobin Liu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun Su
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiakai Liao
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA
| | - Yoshito Oka
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
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30
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Rensing SA. Plant Evo-Devo: How Tip Growth Evolved. Curr Biol 2016; 26:R1228-R1230. [PMID: 27923130 DOI: 10.1016/j.cub.2016.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Apical elongation of polarized plant cells (tip growth) occurs in root hairs of flowering plants and in rhizoids of bryophytes. A new report shows that the formation of these cells relies on genes already present in the first land plants.
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31
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Holtkotte X, Dieterle S, Kokkelink L, Artz O, Leson L, Fittinghoff K, Hayama R, Ahmad M, Hoecker U. Mutations in the N-terminal kinase-like domain of the repressor of photomorphogenesis SPA1 severely impair SPA1 function but not light responsiveness in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:205-218. [PMID: 27310313 DOI: 10.1111/tpj.13241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 05/23/2023]
Abstract
The COP1/SPA complex is an E3 ubiquitin ligase that acts as a key repressor of photomorphogenesis in dark-grown plants. While both COP1 and the four SPA proteins contain coiled-coil and WD-repeat domains, SPA proteins differ from COP1 in carrying an N-terminal kinase-like domain that is not present in COP1. Here, we have analyzed the effects of deletions and missense mutations in the N-terminus of SPA1 when expressed in a spa quadruple mutant background devoid of any other SPA proteins. Deletion of the large N-terminus of SPA1 severely impaired SPA1 activity in transgenic plants with respect to seedling etiolation, leaf expansion and flowering time. This ΔN SPA1 protein showed a strongly reduced affinity for COP1 in vitro and in vivo, indicating that the N-terminus contributes to COP1/SPA complex formation. Deletion of only the highly conserved 95 amino acids of the kinase-like domain did not severely affect SPA1 function nor interactions with COP1 or cryptochromes. In contrast, missense mutations in this part of the kinase-like domain severely abrogated SPA1 function, suggesting an overriding negative effect of these mutations on SPA1 activity. We therefore hypothesize that the sequence of the kinase-like domain has been conserved during evolution because it carries structural information important for the activity of SPA1 in darkness. The N-terminus of SPA1 was not essential for light responsiveness of seedlings, suggesting that photoreceptors can inhibit the COP1/SPA complex in the absence of the SPA1 N-terminal domain. Together, these results uncover an important, but complex role of the SPA1 N-terminus in the suppression of photomorphogenesis.
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Affiliation(s)
- Xu Holtkotte
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stefan Dieterle
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Leonie Kokkelink
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Oliver Artz
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lisa Leson
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Kirsten Fittinghoff
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Ryosuke Hayama
- Max Planck Institute of Plant Breeding Research and Cluster of Excellence on Plant Sciences (CEPLAS), Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Margaret Ahmad
- UMR 8256 (B2A) CNRS - UPMC, IBPS, Université Pierre et Marie Curie, Bat C 3éme étage, 9 quai Saint-Bernard, 75252, Paris, Cedex 05, France
| | - 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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32
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Menon C, Sheerin DJ, Hiltbrunner A. SPA proteins: SPAnning the gap between visible light and gene expression. PLANTA 2016; 244:297-312. [PMID: 27100111 DOI: 10.1007/s00425-016-2509-3] [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: 01/03/2016] [Accepted: 03/26/2016] [Indexed: 05/23/2023]
Abstract
In this review we focus on the role of SPA proteins in light signalling and discuss different aspects, including molecular mechanisms, specificity, and evolution. The ability of plants to perceive and respond to their environment is key to their survival under ever-changing conditions. The abiotic factor light is of particular importance for plants. Light provides plants energy for carbon fixation through photosynthesis, but also is a source of information for the adaptation of growth and development to the environment. Cryptochromes and phytochromes are major photoreceptors involved in control of developmental decisions in response to light cues, including seed germination, seedling de-etiolation, and induction of flowering. The SPA protein family acts in complex with the E3 ubiquitin ligase COP1 to target positive regulators of light responses for degradation by the 26S proteasome to suppress photomorphogenic development in darkness. Light-activated cryptochromes and phytochromes both repress the function of COP1, allowing accumulation of positive photomorphogenic factors in light. In this review, we highlight the role of the SPA proteins in this process and discuss recent advances in understanding how SPAs link light-activation of photoreceptors and downstream signaling.
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Affiliation(s)
- Chiara Menon
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - David J Sheerin
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany.
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Chen S, Wirthmueller L, Stauber J, Lory N, Holtkotte X, Leson L, Schenkel C, Ahmad M, Hoecker U. The functional divergence between SPA1 and SPA2 in Arabidopsis photomorphogenesis maps primarily to the respective N-terminal kinase-like domain. BMC PLANT BIOLOGY 2016; 16:165. [PMID: 27444995 PMCID: PMC4957354 DOI: 10.1186/s12870-016-0854-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plants have evolved complex mechanisms to adapt growth and development to the light environment. The COP1/SPA complex is a key repressor of photomorphogenesis in dark-grown Arabidopsis plants and acts as an E3 ubiquitin ligase to ubiquitinate transcription factors involved in the light response. In the light, COP1/SPA activity is inhibited by photoreceptors, thereby allowing accumulation of these transcription factors and a subsequent light response. Previous results have shown that the four members of the SPA family exhibit partially divergent functions. In particular, SPA1 and SPA2 strongly differ in their responsiveness to light, while they have indistinguishable activities in darkness. The much higher light-responsiveness of SPA2 is partially explained by the much stronger light-induced degradation of SPA2 when compared to SPA1. Here, we have conducted SPA1/SPA2 domain swap experiments to identify the protein domain(s) responsible for the functional divergence between SPA1 and SPA2. RESULTS We have individually swapped the three domains between SPA1 and SPA2 - the N-terminal kinase-like domain, the coiled-coil domain and the WD-repeat domain - and expressed them in spa mutant Arabidopsis plants. The phenotypes of transgenic seedlings show that the respective N-terminal kinase-like domain is primarily responsible for the respective light-responsiveness of SPA1 and SPA2. Furthermore, the most divergent part of the N-terminal domain was sufficient to confer a SPA1- or SPA2-like activity to the respective SPA protein. The stronger light-induced degradation of SPA2 when compared to SPA1 was also primarily conferred by the SPA2 N-terminal domain. At last, the different affinities of SPA1 and SPA2 for cryptochrome 2 are defined by the N-terminal domain of the respective SPA protein. In contrast, both SPA1 and SPA2 similarly interacted with COP1 in light-grown seedlings. CONCLUSIONS Our results show that the distinct activities and protein stabilities of SPA1 and SPA2 in light-grown seedlings are primarily encoded by their N-terminal kinase-like domains. Similarly, the different affinities of SPA1 and SPA2 for cry2 are explained by their respective N-terminal domain. Hence, after a duplication event during evolution, the N-terminal domains of SPA1 and SPA2 underwent subfunctionalization, possibly to allow optimal adaptation of growth and development to a changing light environment.
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Affiliation(s)
- Song Chen
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
- />Present Address: Department of Botany and Plant Biology, University of Geneva, Sciences III, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
| | - Lennart Wirthmueller
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
- />Present Address: Department of Plant Biochemistry, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 12-16, Berlin, Germany
| | - Johannes Stauber
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Niels Lory
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Xu Holtkotte
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Lisa Leson
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Christian Schenkel
- />Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Margaret Ahmad
- />UMR 8256 (B2A) CNRS - UPMC, IBPS, Université Pierre et Marie Curie, Bat C, 9 quai Saint-Bernard, 75252 Paris Cedex 05, France
| | - 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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Tilbrook K, Dubois M, Crocco CD, Yin R, Chappuis R, Allorent G, Schmid-Siegert E, Goldschmidt-Clermont M, Ulm R. UV-B Perception and Acclimation in Chlamydomonas reinhardtii. THE PLANT CELL 2016; 28:966-83. [PMID: 27020958 PMCID: PMC4863380 DOI: 10.1105/tpc.15.00287] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 03/25/2016] [Indexed: 05/03/2023]
Abstract
Plants perceive UV-B, an intrinsic component of sunlight, via a signaling pathway that is mediated by the photoreceptor UV RESISTANCE LOCUS8 (UVR8) and induces UV-B acclimation. To test whether similar UV-B perception mechanisms exist in the evolutionarily distant green alga Chlamydomonas reinhardtii, we identified Chlamydomonas orthologs of UVR8 and the key signaling factor CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1). Cr-UVR8 shares sequence and structural similarity to Arabidopsis thaliana UVR8, has conserved tryptophan residues for UV-B photoreception, monomerizes upon UV-B exposure, and interacts with Cr-COP1 in a UV-B-dependent manner. Moreover, Cr-UVR8 can interact with At-COP1 and complement the Arabidopsis uvr8 mutant, demonstrating that it is a functional UV-B photoreceptor. Chlamydomonas shows apparent UV-B acclimation in colony survival and photosynthetic efficiency assays. UV-B exposure, at low levels that induce acclimation, led to broad changes in the Chlamydomonas transcriptome, including in genes related to photosynthesis. Impaired UV-B-induced activation in the Cr-COP1 mutant hit1 indicates that UVR8-COP1 signaling induces transcriptome changes in response to UV-B. Also, hit1 mutants are impaired in UV-B acclimation. Chlamydomonas UV-B acclimation preserved the photosystem II core proteins D1 and D2 under UV-B stress, which mitigated UV-B-induced photoinhibition. These findings highlight the early evolution of UVR8 photoreceptor signaling in the green lineage to induce UV-B acclimation and protection.
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Affiliation(s)
- Kimberley Tilbrook
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Marine Dubois
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Carlos D Crocco
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Ruohe Yin
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Richard Chappuis
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Guillaume Allorent
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Emanuel Schmid-Siegert
- SIB-Swiss Institute of Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Michel Goldschmidt-Clermont
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Roman Ulm
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211 Geneva 4, Switzerland
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Sun Y, Xu W, Jia Y, Wang M, Xia G. The wheat TaGBF1 gene is involved in the blue-light response and salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1219-30. [PMID: 26588879 DOI: 10.1111/tpj.13082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 05/14/2023]
Abstract
Light and abiotic stress both strongly modulate plant growth and development. However, the effect of light-responsive factors on growth and abiotic stress responses in wheat (Triticum aestivum) is unknown. G-box binding factors (GBFs) are blue light-specific components, but their function in abiotic stress responses has not been studied. Here we identified a wheat GBF1 gene that mediated both the blue light- and abiotic stress-responsive signaling pathways. TaGBF1 was inducible by blue light, salt and exposure to abscisic acid (ABA). TaGBF1 interacted with a G-box light-responsive element in vitro and promoted a blue-light response in wheat and Aradidopsis thaliana. Both TaGBF1 over-expression in wheat and its heterologous expression in A. thaliana heighten sensitivity to salinity and ABA, but its knockdown in wheat conferred resistance to high salinity and ABA. The expression of AtABI5, a key component of the ABA signaling pathway in A. thaliana, and its homolog Wabi5 in wheat was increased by transgenic expression of TaGBF1. The hypersensitivity to salt and ABA caused by TaGBF1 was not observed in the abi5 mutant background, showing that ABI5 is the mediator in TaGBF1-induced abiotic stress responses. However, the hypersensitivity to salt conferred by TaGBF1 is not dependent on light. This suggests that TaGBF1 is a common component of blue light- and abiotic stress-responsive signaling pathways.
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Affiliation(s)
- Yang Sun
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong, 250100, China
| | - Wei Xu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong, 250100, China
| | - Yuebin Jia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong, 250100, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong, 250100, China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong, 250100, China
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Chen S, Lory N, Stauber J, Hoecker U. Photoreceptor Specificity in the Light-Induced and COP1-Mediated Rapid Degradation of the Repressor of Photomorphogenesis SPA2 in Arabidopsis. PLoS Genet 2015; 11:e1005516. [PMID: 26368289 PMCID: PMC4569408 DOI: 10.1371/journal.pgen.1005516] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/19/2015] [Indexed: 11/18/2022] Open
Abstract
The Arabidopsis COP1/SPA E3 ubiquitin ligase is a key negative regulator that represses light signaling in darkness by targeting transcription factors involved in the light response for degradation. The COP1/SPA complex consists of COP1 and members of the four-member SPA protein family (SPA1-SPA4). Genetic analysis indicated that COP1/SPA2 function is particularly strongly repressed by light when compared to complexes carrying the other three SPAs, thereby promoting a light response after exposure of plants to extremely low light. Here, we show that the SPA2 protein is degraded within 5–15 min after exposure of dark-grown seedlings to a pulse of light. Phytochrome photoreceptors are required for the rapid degradation of SPA2 in red, far-red and also in blue light, whereas cryptochromes are not involved in the rapid, blue light-induced reduction in SPA2 protein levels. These results uncover a photoreceptor-specific mechanism of light-induced inhibition of COP1/SPA2 function. Phytochrome A (phyA) is required for the severe blue light responsiveness of spa triple mutants expressing only SPA2, thus confirming the important role of phyA in downregulating SPA2 function in blue light. In blue light, SPA2 forms a complex with cryptochrome 1 (cry1), but not with cryptochrome 2 (cry2) in vivo, indicating that the lack of a rapid blue light response of the SPA2 protein is only in part caused by a failure to interact with cryptochromes. Since SPA1 interacts with both cry1 and cry2, these results provide first molecular evidence that the light-regulation of different SPA proteins diverged during evolution. SPA2 degradation in the light requires COP1 and the COP1-interacting coiled-coil domain of SPA2, supporting that SPA2 is ubiquitinated by COP1. We propose that light perceived by phytochromes causes a switch in the ubiquitination activity of COP1/SPA2 from ubiquitinating downstream substrates to ubiquitinating SPA2, which subsequently causes a repression of COP1/SPA2 function. Plants have evolved photoreceptors that initiate a signaling cascade to adjust growth and development to the ambient light environment. The CUL4-dependent COP1/SPA E3 ubiquitin ligase is a key negative regulator of light signaling whose function is repressed by light. Recent research has identified mechanisms that are common to both phytochrome and cryptochrome photoreceptors. Here, we have identified a mechanism of light-induced COP1/SPA repression that is specific to phytochrome photoreceptors. We show that the SPA2 protein is very rapidly degraded in red, far-red and blue light in a phytochrome-dependent fashion. We further show that SPA2 degradation in the light depends on COP1 and on the interaction of SPA2 with COP1. Hence, our results suggest a light-induced degradation of SPA2, but not of COP1, by the COP1/SPA2 ubiquitin ligase. The human ortholog of COP1, which functions without the plant-specific SPA proteins, is known to be regulated by autodegradation following DNA damage. Hence, autodegradation of components of this E3 ligase is a regulatory mechanism used in both humans and plants.
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Affiliation(s)
- Song Chen
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
| | - Niels Lory
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
| | - Johannes Stauber
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
- * E-mail:
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Song YH, Shim JS, Kinmonth-Schultz HA, Imaizumi T. Photoperiodic flowering: time measurement mechanisms in leaves. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:441-64. [PMID: 25534513 PMCID: PMC4414745 DOI: 10.1146/annurev-arplant-043014-115555] [Citation(s) in RCA: 387] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many plants use information about changing day length (photoperiod) to align their flowering time with seasonal changes to increase reproductive success. A mechanism for photoperiodic time measurement is present in leaves, and the day-length-specific induction of the FLOWERING LOCUS T (FT) gene, which encodes florigen, is a major final output of the pathway. Here, we summarize the current understanding of the molecular mechanisms by which photoperiodic information is perceived in order to trigger FT expression in Arabidopsis as well as in the primary cereals wheat, barley, and rice. In these plants, the differences in photoperiod are measured by interactions between circadian-clock-regulated components, such as CONSTANS (CO), and light signaling. The interactions happen under certain day-length conditions, as previously predicted by the external coincidence model. In these plants, the coincidence mechanisms are governed by multilayered regulation with numerous conserved as well as unique regulatory components, highlighting the breadth of photoperiodic regulation across plant species.
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Affiliation(s)
- Young Hun Song
- Department of Biology, University of Washington, Seattle, Washington 98195-1800;
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