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Péter C, Nagy F, Viczián A. SUMOylation of different targets fine-tunes phytochrome signaling. THE NEW PHYTOLOGIST 2021; 232:1201-1211. [PMID: 34289130 DOI: 10.1111/nph.17634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.
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Affiliation(s)
- Csaba Péter
- Laboratory of Photo and Chronobiology, Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Laboratory of Photo and Chronobiology, Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - András Viczián
- Laboratory of Photo and Chronobiology, Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
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2
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Abstract
The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis.
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Affiliation(s)
- Mei-Chun Cheng
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Inyup Paik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
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3
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Song Q, Lee J, Akter S, Rogers M, Grene R, Li S. Prediction of condition-specific regulatory genes using machine learning. Nucleic Acids Res 2020; 48:e62. [PMID: 32329779 PMCID: PMC7293043 DOI: 10.1093/nar/gkaa264] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/19/2020] [Accepted: 04/20/2020] [Indexed: 12/31/2022] Open
Abstract
Recent advances in genomic technologies have generated data on large-scale protein-DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5-25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.
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Affiliation(s)
- Qi Song
- Graduate program in Genetics, Bioinformatics and Computational Biology. Virginia Tech., Blacksburg, VA 24061, USA
| | - Jiyoung Lee
- Graduate program in Genetics, Bioinformatics and Computational Biology. Virginia Tech., Blacksburg, VA 24061, USA
| | - Shamima Akter
- School of Plant and Environmental Sciences. Virginia Tech., Blacksburg, VA 24061, USA
| | - Matthew Rogers
- Department of Statistics. Virginia Tech., Blacksburg, VA 24061, USA
| | - Ruth Grene
- Graduate program in Genetics, Bioinformatics and Computational Biology. Virginia Tech., Blacksburg, VA 24061, USA
- School of Plant and Environmental Sciences. Virginia Tech., Blacksburg, VA 24061, USA
| | - Song Li
- Graduate program in Genetics, Bioinformatics and Computational Biology. Virginia Tech., Blacksburg, VA 24061, USA
- School of Plant and Environmental Sciences. Virginia Tech., Blacksburg, VA 24061, USA
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Qu GP, Li H, Lin XL, Kong X, Hu ZL, Jin YH, Liu Y, Song HL, Kim DH, Lin R, Li J, Jin JB. Reversible SUMOylation of FHY1 Regulates Phytochrome A Signaling in Arabidopsis. MOLECULAR PLANT 2020; 13:879-893. [PMID: 32298785 DOI: 10.1016/j.molp.2020.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/15/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
In response to far-red light (FR), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) transports the photoactivated phytochrome A (phyA), the primary FR photoreceptor, into the nucleus, where it initiates FR signaling in plants. Light promotes the 26S proteasome-mediated degradation of FHY1, which desensitizes FR signaling, but the underlying regulatory mechanism remains largely unknown. Here, we show that reversible SUMOylation of FHY1 tightly regulates this process. Lysine K32 (K32) and K103 are major SUMOylation sites of FHY1. We found that FR exposure promotes the SUMOylation of FHY1, which accelerates its degradation. Furthermore, we discovered that ARABIDOPSIS SUMO PROTEASE 1 (ASP1) interacts with FHY1 in the nucleus under FR and facilitates its deSUMOylation. FHY1 was strongly SUMOylated and its protein level was decreased in the asp1-1 loss-of-function mutant compared with that in the wild type under FR. Consistently, asp1-1 seedlings exhibited a decreased sensitivity to FR, suggesting that ASP1 plays an important role in the maintenance of proper FHY1 levels under FR. Genetic analysis further revealed that ASP1 regulates FR signaling through an FHY1- and phyA-dependent pathway. Interestingly, We found that continuous FR inhibits ASP1 accumulation, perhaps contributing to the desensitization of FR signaling. Taken together, these results indicate that FR-induced SUMOylation and ASP1-dependent deSUMOylation of FHY1 represent a key regulatory mechanism that fine-tunes FR signaling.
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Affiliation(s)
- Gao-Ping Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiao-Li Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiangxiong Kong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zi-Liang Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yin Hua Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hang-Lin Song
- Yanbian Academy of Agriculture Sciences, Yanji 133001, China
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon 57922, South Korea
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Menon C, Klose C, Hiltbrunner A. Arabidopsis FHY1 and FHY1-LIKE Are Not Required for Phytochrome A Signal Transduction in the Nucleus. PLANT COMMUNICATIONS 2020; 1:100007. [PMID: 33404546 PMCID: PMC7748001 DOI: 10.1016/j.xplc.2019.100007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/27/2019] [Accepted: 11/06/2019] [Indexed: 05/13/2023]
Abstract
Photoreceptors of the phytochrome family control a multitude of responses in plants. Phytochrome A (phyA) is essential for far-red light perception, which is important for germination and seedling establishment in strong canopy shade. Translocation of phyA from the cytosol into nucleus is a key step in far-red light signaling and requires FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). FHY1/FHL bind to phyA downstream signaling components. Therefore, it has been suggested that FHY1/FHL also have a function in assembling phyA transcription factor complexes in the nucleus. Yet, in this study, we show that constitutively nuclear-localized phyA is active in the absence of FHY1 and FHL. Furthermore, an artificial FHY1, consisting of an SV40 NLS, a phyA binding site, and a YFP tag as spacer between them, complements the fhy1-3 fhl-1 double mutant. These findings show that FHY1 and FHL are not required for phyA downstream signaling in the nucleus. However, we found that lines expressing phyA-NLS-YFP are hypersensitive to red and far-red light and that slightly increased levels of constitutively nuclear-localized phyA result in photomorphogenic development in the dark. Thus, restricting phyA to the cytosol and inducing nuclear transport in light by interaction with FHY1/FHL might be important to suppress photomorphogenesis in the dark.
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Affiliation(s)
- Chiara Menon
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Cornelia Klose
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Corresponding author
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6
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Sheerin DJ, Hiltbrunner A. Molecular mechanisms and ecological function of far-red light signalling. PLANT, CELL & ENVIRONMENT 2017; 40:2509-2529. [PMID: 28102581 DOI: 10.1111/pce.12915] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 05/18/2023]
Abstract
Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.
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Affiliation(s)
- David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
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7
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Hämälä T, Mattila TM, Leinonen PH, Kuittinen H, Savolainen O. Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata. Mol Ecol 2017; 26:3484-3496. [PMID: 28393414 DOI: 10.1111/mec.14135] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/25/2017] [Accepted: 03/29/2017] [Indexed: 12/25/2022]
Abstract
Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in postdormancy germination in A. thaliana. The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F1 and F2 progenies suggests that Bateson-Dobzhansky-Muller incompatibilities likely act through uniparentally inherited factors. Examination of genomewide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Päivi H Leinonen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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Burgess SJ, Granero-Moya I, Grangé-Guermente MJ, Boursnell C, Terry MJ, Hibberd JM. Ancestral light and chloroplast regulation form the foundations for C 4 gene expression. NATURE PLANTS 2016; 2:16161. [PMID: 27748771 DOI: 10.1038/nplants.2016.161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
C4 photosynthesis acts as a carbon concentrating mechanism that leads to large increases in photosynthetic efficiency. The C4 pathway is found in more than 60 plant lineages1 but the molecular enablers of this evolution are poorly understood. In particular, it is unclear how non-photosynthetic proteins in the ancestral C3 system have repeatedly become strongly expressed and integrated into photosynthesis gene regulatory networks in C4 leaves. Here, we provide clear evidence that in C3 leaves, genes encoding key enzymes of the C4 pathway are already co-regulated with photosynthesis genes and are controlled by both light and chloroplast-to-nucleus signalling. In C4 leaves this regulation becomes increasingly dependent on the chloroplast. We propose that regulation of C4 cycle genes by light and the chloroplast in the ancestral C3 state has facilitated the repeated evolution of the complex and convergent C4 trait.
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Affiliation(s)
- Steven J Burgess
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Ignasi Granero-Moya
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Chris Boursnell
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Matthew J Terry
- Biological Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Julian M Hibberd
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
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FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. Proc Natl Acad Sci U S A 2016; 113:9375-80. [PMID: 27469166 DOI: 10.1073/pnas.1602960113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Plant meristems are responsible for the generation of all plant tissues and organs. Here we show that the transcription factor (TF) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) plays an important role in both floral meristem (FM) determinacy and shoot apical meristem maintenance in Arabidopsis, in addition to its well-known multifaceted roles in plant growth and development during the vegetative stage. Through genetic analyses, we show that WUSCHEL (WUS) and CLAVATA3 (CLV3), two central players in the establishment and maintenance of meristems, are epistatic to FHY3 Using genome-wide ChIP-seq and RNA-seq data, we identify hundreds of FHY3 target genes in flowers and find that FHY3 mainly acts as a transcriptional repressor in flower development, in contrast to its transcriptional activator role in seedlings. Binding motif-enrichment analyses indicate that FHY3 may coregulate flower development with three flower-specific MADS-domain TFs and four basic helix-loop-helix TFs that are involved in photomorphogenesis. We further demonstrate that CLV3, SEPALLATA1 (SEP1), and SEP2 are FHY3 target genes. In shoot apical meristem, FHY3 directly represses CLV3, which consequently regulates WUS to maintain the stem cell pool. Intriguingly, CLV3 expression did not change significantly in fhy3 and phytochrome B mutants before and after light treatment, indicating that FHY3 and phytochrome B are involved in light-regulated meristem activity. In FM, FHY3 directly represses CLV3, but activates SEP2, to ultimately promote FM determinacy. Taken together, our results reveal insights into the mechanisms of meristem maintenance and determinacy, and illustrate how the roles of a single TF may vary in different organs and developmental stages.
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