1
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Willige BC, Yoo CY, Saldierna Guzmán JP. What is going on inside of phytochrome B photobodies? THE PLANT CELL 2024; 36:2065-2085. [PMID: 38511271 PMCID: PMC11132900 DOI: 10.1093/plcell/koae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 03/22/2024]
Abstract
Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.
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Affiliation(s)
- Björn Christopher Willige
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, UT 84112, USA
| | - Jessica Paola Saldierna Guzmán
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
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2
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Li Y, Guo Y, Cao Y, Xia P, Xu D, Sun N, Jiang L, Dong J. Temporal control of the Aux/IAA genes BnIAA32 and BnIAA34 mediates Brassica napus dual shade responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:928-942. [PMID: 37929685 DOI: 10.1111/jipb.13582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/04/2023] [Indexed: 11/07/2023]
Abstract
Precise responses to changes in light quality are crucial for plant growth and development. For example, hypocotyls of shade-avoiding plants typically elongate under shade conditions. Although this typical shade-avoidance response (TSR) has been studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanisms underlying shade tolerance are poorly understood. Here we report that B. napus (Brassica napus) seedlings exhibit dual shade responses. In addition to the TSR, B. napus seedlings also display an atypical shade response (ASR), with shorter hypocotyls upon perception of early-shade cues. Genome-wide selective sweep analysis indicated that ASR is associated with light and auxin signaling. Moreover, genetic studies demonstrated that phytochrome A (BnphyA) promotes ASR, whereas BnphyB inhibits it. During ASR, YUCCA8 expression is activated by early-shade cues, leading to increased auxin biosynthesis. This inhibits hypocotyl elongation, as young B. napus seedlings are highly sensitive to auxin. Notably, two non-canonical AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressor genes, BnIAA32 and BnIAA34, are expressed during this early stage. BnIAA32 and BnIAA34 inhibit hypocotyl elongation under shade conditions, and mutations in BnIAA32 and BnIAA34 suppress ASR. Collectively, our study demonstrates that the temporal expression of BnIAA32 and BnIAA34 determines the behavior of B. napus seedlings following shade-induced auxin biosynthesis.
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Affiliation(s)
- Yafei Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yiyi Guo
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yue Cao
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Sun
- Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Lixi Jiang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Dong
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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3
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Huq E, Lin C, Quail PH. Light signaling in plants-a selective history. PLANT PHYSIOLOGY 2024; 195:213-231. [PMID: 38431282 PMCID: PMC11060691 DOI: 10.1093/plphys/kiae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.
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Affiliation(s)
- Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA 94710, USA
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4
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Kim RJA, Fan D, He J, Kim K, Du J, Chen M. Photobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization. Nat Commun 2024; 15:3519. [PMID: 38664420 PMCID: PMC11045832 DOI: 10.1038/s41467-024-47790-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions - PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm - which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.
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Affiliation(s)
- Ruth Jean Ae Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - De Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jiangman He
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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5
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Ji Z, Belfield EJ, Li S, Fu X, Harberd NP. Discovery of a second-site nia2 mutation in the background of multiple Arabidopsis PIF-related mutants containing the pif3-3 allele. THE NEW PHYTOLOGIST 2024; 241:17-23. [PMID: 37891447 PMCID: PMC10952432 DOI: 10.1111/nph.19344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Zhe Ji
- Department of BiologyUniversity of OxfordOxfordOX1 3RBUK
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | | | - Shan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing210095China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- New Cornerstone Science LaboratoryBeijing100101China
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6
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Xie Y, Liu W, Liang W, Ling X, Ma J, Yang C, Li L. Phytochrome B inhibits the activity of phytochrome-interacting factor 7 involving phase separation. Cell Rep 2023; 42:113562. [PMID: 38071618 DOI: 10.1016/j.celrep.2023.113562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Shade-intolerant plants sense changes in the light environment and trigger shade-avoidance syndrome in the presence of neighboring vegetation. Phytochrome-interacting factor 7 (PIF7) is an essential regulator that integrates shade signals into plant transcriptional networks. While the regulation of PIF7 under shade conditions has been well studied, the mechanism that represses PIF7 activity under white light remains ambiguous. Here, we report that PIF7 forms nuclear puncta containing phase-separated liquid-like condensates. Phytochrome B (phyB) then binds to dephosphorylated PIF7 and promotes its condensed phase of PIF7 under white light. The phyB-PIF7 condensate subsequently inhibits the DNA-binding activity of PIF7. However, shade inactivation of phyB causes the dissociation of phyB-PIF7 condensates and allows unbound PIF7 to promote the transcription of shade-induced genes. This reversible transcriptional condensation via phase separation provides sessile organisms with the flexibility of gene control to adapt to their surrounding environment.
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Affiliation(s)
- Yu Xie
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenbo Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenjing Liang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaobin Ling
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Chuanwei Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China.
| | - Lin Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China.
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7
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Guo Q, Jing Y, Gao Y, Liu Y, Fang X, Lin R. The PIF1/PIF3-MED25-HDA19 transcriptional repression complex regulates phytochrome signaling in Arabidopsis. THE NEW PHYTOLOGIST 2023; 240:1097-1115. [PMID: 37606175 DOI: 10.1111/nph.19205] [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: 06/16/2023] [Accepted: 07/25/2023] [Indexed: 08/23/2023]
Abstract
Light signals are perceived by photoreceptors, triggering the contrasting developmental transition in dark-germinated seedlings. Phytochrome-interacting factors (PIFs) are key regulators of this transition. Despite their prominent functions in transcriptional activation, little is known about PIFs' roles in transcriptional repression. Here, we provide evidence that histone acetylation is involved in regulating phytochrome-PIFs signaling in Arabidopsis. The histone deacetylase HDA19 interacts and forms a complex with PIF1 and PIF3 and the Mediator subunit MED25. The med25/hda19 double mutant mimics and enhances the phenotype of pif1/pif3 in both light and darkness. HDA19 and MED25 are recruited by PIF1/PIF3 to the target loci to reduce histone acetylation and chromatin accessibility, providing a mechanism for PIF1/PIF3-mediated transcriptional repression. Furthermore, MED25 forms liquid-like condensates, which can compartmentalize PIF1/PIF3 and HDA19 in vitro and in vivo, and the number of MED25 puncta increases in darkness. Collectively, our study establishes a mechanism wherein PIF1/PIF3 interact with HDA19 and MED25 to mediate transcriptional repression in the phytochrome signaling pathway and suggests that condensate formation with Mediator may explain the distinct and specific transcriptional activity of PIF proteins.
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Affiliation(s)
- Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuan Gao
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yitong Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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8
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Zhao Y, Zheng X, Zhang X, Wang W, Cai G, Bi G, Chen S, Sun C, Zhou JM. PIF3 is phosphorylated by MAPK to modulate plant immunity. THE NEW PHYTOLOGIST 2023; 240:372-381. [PMID: 37475167 DOI: 10.1111/nph.19139] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Surface-localized pattern recognition receptors perceive pathogen-associated molecular patterns (PAMPs) to activate pattern-triggered immunity (PTI). Activation of mitogen-activated protein kinases (MAPKs) represents a major PTI response. Here, we report that Arabidopsis thaliana PIF3 negatively regulates plant defense gene expression and resistance to Pseudomonas syringae DC3000. PAMPs trigger phosphorylation of PIF3. Further study reveals that PIF3 interacts with and is phosphorylated by MPK3/6. By mass spectrometry and site-directed mutagenesis, we identified the corresponding phosphorylation sites which fit for SP motif. We further show that a phospho-mimicking PIF3 variant (PIF36D /pifq) conferred increased susceptibility to P. syringae DC3000 and caused lower levels of defense gene expression in plants. Together, this study reveals that PIF3 is phosphorylated by MPK3/6 and phosphorylation of the SP motif residues is required for its negative regulation on plant immunity.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Xiaojuan Zheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gaihong Cai
- National Institute of Biological Sciences, Beijing, 100101, China
| | - Guozhi Bi
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 100101, China
| | - Chuanqing Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
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9
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Liu W, Lowrey H, Leung CC, Adamchek C, Du J, He J, Chen M, Gendron JM. The circadian clock regulates PIF3 protein stability in parallel to red light. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558326. [PMID: 37781622 PMCID: PMC10541125 DOI: 10.1101/2023.09.18.558326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The circadian clock is an endogenous oscillator, but its importance lies in its ability to impart rhythmicity on downstream biological processes or outputs. Focus has been placed on understanding the core transcription factors of the circadian clock and how they connect to outputs through regulated gene transcription. However, far less is known about posttranslational mechanisms that tether clocks to output processes through protein regulation. Here, we identify a protein degradation mechanism that tethers the clock to photomorphogenic growth. By performing a reverse genetic screen, we identify a clock-regulated F-box type E3 ubiquitin ligase, CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1 ( CFH1 ), that controls hypocotyl length. We then show that CFH1 functions in parallel to red light signaling to target the transcription factor PIF3 for degradation. This work demonstrates that the circadian clock is tethered to photomorphogenesis through the ubiquitin proteasome system and that PIF3 protein stability acts as a hub to integrate information from multiple environmental signals.
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10
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Yuan DP, Yang S, Feng L, Chu J, Dong H, Sun J, Chen H, Li Z, Yamamoto N, Zheng A, Li S, Yoon HC, Chen J, Ma D, Xuan YH. Red-light receptor phytochrome B inhibits BZR1-NAC028-CAD8B signaling to negatively regulate rice resistance to sheath blight. PLANT, CELL & ENVIRONMENT 2023; 46:1249-1263. [PMID: 36457051 DOI: 10.1111/pce.14502] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Phytochrome (Phy)-regulated light signalling plays important roles in plant growth, development, and stress responses. However, its function in rice defence against sheath blight disease (ShB) remains unclear. Here, we found that PhyB mutation or shade treatment promoted rice resistance to ShB, while resistance was reduced by PhyB overexpression. Further analysis showed that PhyB interacts with phytochrome-interacting factor-like 15 (PIL15), brassinazole resistant 1 (BZR1), and vascular plant one-zinc-finger 2 (VOZ2). Plants overexpressing PIL15 were more susceptible to ShB in contrast to bzr1-D-overexpressing plants compared with the wild-type, suggesting that PhyB may inhibit BZR1 to negatively regulate rice resistance to ShB. Although BZR1 is known to regulate brassinosteroid (BR) signalling, the observation that BR signalling negatively regulated resistance to ShB indicated an independent role for BZR1 in controlling rice resistance. It was also found that the BZR1 ligand NAC028 positively regulated resistance to ShB. RNA sequencing showed that cinnamyl alcohol dehydrogenase 8B (CAD8B), involved in lignin biosynthesis was upregulated in both bzr1-D- and NAC028-overexpressing plants compared with the wild-type. Yeast-one hybrid, ChIP, and transactivation assays demonstrated that BZR1 and NAC028 activate CAD8B directly. Taken together, the analyses demonstrated that PhyB-mediated light signalling inhibits the BZR1-NAC028-CAD8B pathway to regulate rice resistance to ShB.
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Affiliation(s)
- De Peng Yuan
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shuo Yang
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Lu Feng
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Jin Chu
- Laboratory of Rice Disease Research, Institution of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Hai Dong
- Laboratory of Rice Disease Research, Institution of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jian Sun
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Huan Chen
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zhuo Li
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Naoki Yamamoto
- Department of Plant Protection, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Aiping Zheng
- Department of Plant Protection, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shuang Li
- Department of Biological Science, College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | | | - Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Dianrong Ma
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Yuan Hu Xuan
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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11
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Kim C, Kwon Y, Jeong J, Kang M, Lee GS, Moon JH, Lee HJ, Park YI, Choi G. Phytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins. Nat Commun 2023; 14:1708. [PMID: 36973259 PMCID: PMC10042835 DOI: 10.1038/s41467-023-37421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Phytochrome B (phyB) is a plant photoreceptor that forms a membraneless organelle called a photobody. However, its constituents are not fully known. Here, we isolated phyB photobodies from Arabidopsis leaves using fluorescence-activated particle sorting and analyzed their components. We found that a photobody comprises ~1,500 phyB dimers along with other proteins that could be classified into two groups: The first includes proteins that directly interact with phyB and localize to the photobody when expressed in protoplasts, while the second includes proteins that interact with the first group proteins and require co-expression of a first-group protein to localize to the photobody. As an example of the second group, TOPLESS interacts with PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and localizes to the photobody when co-expressed with PCH1. Together, our results support that phyB photobodies include not only phyB and its primary interacting proteins but also its secondary interacting proteins.
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Affiliation(s)
- Chanhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Yongmin Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Jaehoon Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Minji Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Ga Seul Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk, 28160, Korea
| | - Jeong Hee Moon
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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12
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Sang Q, Fan L, Liu T, Qiu Y, Du J, Mo B, Chen M, Chen X. MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis. Nat Commun 2023; 14:1449. [PMID: 36949101 PMCID: PMC10033679 DOI: 10.1038/s41467-023-36774-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/14/2023] [Indexed: 03/24/2023] Open
Abstract
MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remain ambiguous. Here we show that HYPONASTIC LEAVES 1 (HYL1)-a key component of miRNA biogenesis-acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in the temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 allele that rescues hyl1-2's defects in miRNA biogenesis and thermoresponsive hypocotyl elongation. Genome-wide miRNA and transcriptome analysis revealed microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE 9 (SPL9) to be critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miR156/SPL9 module as a previously uncharacterized genetic circuit that enables plant growth plasticity in response to environmental temperature and light changes.
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Affiliation(s)
- Qing Sang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of the Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Lusheng Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Tianxiang Liu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of the Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, 100871, China.
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13
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Jia S, Liu X, Wen X, Waheed A, Ding Y, Kahar G, Li X, Zhang D. Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:620. [PMID: 36771705 PMCID: PMC9919239 DOI: 10.3390/plants12030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/15/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.
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Affiliation(s)
- Shanshan Jia
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaojie Liu
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Xuejing Wen
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Abdul Waheed
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Yu Ding
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Gulnaz Kahar
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaoshuang Li
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Daoyuan Zhang
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
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14
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Song P, Yang Z, Guo C, Han R, Wang H, Dong J, Kang D, Guo Y, Yang S, Li J. 14-3-3 proteins regulate photomorphogenesis by facilitating light-induced degradation of PIF3. THE NEW PHYTOLOGIST 2023; 237:140-159. [PMID: 36110045 DOI: 10.1111/nph.18494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
14-3-3s are highly conserved phosphopeptide-binding proteins that play important roles in various developmental and signaling pathways in plants. However, although protein phosphorylation has been proven to be a key mechanism for regulating many pivotal components of the light signaling pathway, the role of 14-3-3 proteins in photomorphogenesis remains largely obscure. PHYTOCHROME-INTERACTING FACTOR3 (PIF3) is an extensively studied transcription factor repressing photomorphogenesis, and it is well-established that upon red (R) light exposure, photo-activated phytochrome B (phyB) interacts with PIF3 and induces its rapid phosphorylation and degradation. PHOTOREGULATORY PROTEIN KINASES (PPKs), a family of nuclear protein kinases, interact with phyB and PIF3 in R light and mediate multisite phosphorylation of PIF3 in vivo. Here, we report that two members of the 14-3-3 protein family, 14-3-3λ and κ, bind to a serine residue in the bHLH domain of PIF3 that can be phosphorylated by PPKs, and act as key positive regulators of R light-induced photomorphogenesis. Moreover, 14-3-3λ and κ preferentially interact with photo-activated phyB and promote the phyB-PIF3-PPK complex formation, thereby facilitating phyB-induced phosphorylation and degradation of PIF3 upon R light exposure. Together, our data demonstrate that 14-3-3λ and κ work in close concert with the phyB-PIF3 module to regulate light signaling in Arabidopsis.
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Affiliation(s)
- Pengyu Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zidan Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Can Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Run Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huaichang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Dingming Kang
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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15
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Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes. Nat Commun 2022; 13:7440. [PMID: 36460634 PMCID: PMC9718756 DOI: 10.1038/s41467-022-35080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Light initiates chloroplast biogenesis in Arabidopsis by eliminating PHYTOCHROME-INTERACTING transcription FACTORs (PIFs), which in turn de-represses nuclear photosynthesis genes, and synchronously, generates a nucleus-to-plastid (anterograde) signal that activates the plastid-encoded bacterial-type RNA polymerase (PEP) to transcribe plastid photosynthesis genes. However, the identity of the anterograde signal remains frustratingly elusive. The main challenge has been the difficulty to distinguish regulators from the plethora of necessary components for plastid transcription and other essential chloroplast functions, such as photosynthesis. Here, we show that the genome-wide induction of nuclear photosynthesis genes is insufficient to activate the PEP. PEP inhibition is imposed redundantly by multiple PIFs and requires PIF3's activator activity. Among the nuclear-encoded components of the PEP holoenzyme, we identify four light-inducible, PIF-repressed sigma factors as anterograde signals. Together, our results elucidate that light-dependent inhibition of PIFs activates plastid photosynthesis genes via sigma factors as anterograde signals in parallel with the induction of nuclear photosynthesis genes.
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16
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Bajracharya A, Xi J, Grace KF, Bayer EE, Grant CA, Clutton CH, Baerson SR, Agarwal AK, Qiu Y. PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosensory growth requires the Mediator subunit MED14. PLANT PHYSIOLOGY 2022; 190:2706-2721. [PMID: 36063057 PMCID: PMC9706435 DOI: 10.1093/plphys/kiac412] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/12/2022] [Indexed: 05/19/2023]
Abstract
While moderately elevated ambient temperatures do not trigger stress responses in plants, they do substantially stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis (Arabidopsis thaliana). Although it is well known that PIF4 and its co-activator HEMERA (HMR) promote plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. In this report, we investigated the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 was identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 was required for the thermal induction of PIF4 target genes but had a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirmed that the expression of numerous PIF4/HMR-dependent, auxin-related genes required MED14 at warm temperatures. Moreover, PIF4 and HMR physically interacted with MED14 and both were indispensable for the association of MED14 with the promoters of these thermoresponsive genes. While PIF4 did not regulate MED14 levels, HMR was required for the transcript abundance of MED14. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature.
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Affiliation(s)
| | - Jing Xi
- Natural Products Utilization Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Oxford, Mississippi, USA
| | - Karlie F Grace
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Eden E Bayer
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Chloe A Grant
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Caroline H Clutton
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Scott R Baerson
- Natural Products Utilization Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Oxford, Mississippi, USA
| | - Ameeta K Agarwal
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA
- Division of Pharmacology, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA
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17
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SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in
Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2214565119. [PMID: 36282917 PMCID: PMC9636961 DOI: 10.1073/pnas.2214565119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Regulation of transcription and pre–messenger RNA (mRNA) splicing is essential for transcript diversity and light-regulated gene expression in plants. Although several transcription factors have been described, only a few splicing factors are known to regulate light signaling pathways. Here, we describe the functional characterization of splicing factor SWAP1, which interacts with two previously characterized splicing factors, SFPS and RRC1, forming a ternary complex. SWAP1 also interacts with photoactivated phytochrome B (phyB). All three single and double mutant combinations display similar hypocotyl lengths under red light. SWAP1 modulates alternative splicing of a large number of genes, and a subset of these genes is coordinately regulated by SFPS, RRC1, and SWAP1. These results highlight the importance of phyB-interacting splicing factors in light-regulated plant development. Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light–absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length–independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swap1sfps, swap1rrc1, and sfpsrrc1 double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swap1sfps double and swap1sfpsrrc1 triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre–messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors.
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18
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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