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Bogomolov A, Zolotareva K, Filonov S, Chadaeva I, Rasskazov D, Sharypova E, Podkolodnyy N, Ponomarenko P, Savinkova L, Tverdokhleb N, Khandaev B, Kondratyuk E, Podkolodnaya O, Zemlyanskaya E, Kolchanov NA, Ponomarenko M. AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L. Int J Mol Sci 2024; 25:607. [PMID: 38203780 PMCID: PMC10779315 DOI: 10.3390/ijms25010607] [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: 10/31/2023] [Revised: 12/18/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.
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Affiliation(s)
- Anton Bogomolov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Sergey Filonov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Natalya Tverdokhleb
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Bato Khandaev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk 630501, Novosibirsk Region, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
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Zhang X, Shen Z, Sun X, Chen M, Zhang N. Integrated analysis of transcriptomic and proteomic data reveals novel regulators of soybean ( Glycine max) hypocotyl development. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:1086-1098. [PMID: 37866377 DOI: 10.1071/fp23013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
Hypocotyl elongation directly affects the seedling establishment and soil-breaking after germination. In soybean (Glycine max ), the molecular mechanisms regulating hypocotyl development remain largely elusive. To decipher the regulatory landscape, we conducted proteome and transcriptome analysis of soybean hypocotyl samples at different development stages. Our results showed that during hypocotyl development, many proteins were with extreme high translation efficiency (TE) and may act as regulators. These potential regulators include multiple peroxidases and cell wall reorganisation related enzymes. Peroxidases may produce ROS including H2 O2 . Interestingly, exogenous H2 O2 application promoted hypocotyl elongation, supporting peroxidases as regulators of hypocotyl development. However, a vast variety of proteins were shown to be with dramatically changed TE during hypocotyl development, including multiple phytochromes, plasma membrane intrinsic proteins (PIPs) and aspartic proteases. Their potential roles in hypocotyl development were confirmed by that ectopic expression of GmPHYA1 and GmPIP1-6 in Arabidopsis thaliana affected hypocotyl elongation. In addition, the promoters of these potential regulatory genes contain multiple light/gibberellin/auxin responsive elements, while the expression of some members in hypocotyls was significantly regulated by light and exogenous auxin/gibberellin. Overall, our results revealed multiple novel regulatory factors of soybean hypocotyl elongation. Further research on these regulators may lead to new approvals to improve soybean hypocotyl traits.
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Affiliation(s)
- Xueliang Zhang
- School of Life Sciences, Henan University, Kaifeng, China
| | - Zhikang Shen
- Sanya Institute, Henan University, Sanya, China; and State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Xiaohu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Min Chen
- Sanya Institute, Henan University, Sanya, China; and State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Naichao Zhang
- School of Life Sciences, Henan University, Kaifeng, China
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Pantazopoulou CK, Buti S, Nguyen CT, Oskam L, Weits DA, Farmer EE, Kajala K, Pierik R. Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics. Nat Commun 2023; 14:5827. [PMID: 37730832 PMCID: PMC10511701 DOI: 10.1038/s41467-023-41530-0] [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: 12/23/2021] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca2+]cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes reduce touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.
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Affiliation(s)
- Chrysoula K Pantazopoulou
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands.
| | - Sara Buti
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Chi Tam Nguyen
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Lisa Oskam
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Daan A Weits
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Kaisa Kajala
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands.
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
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Zhao J, Bo K, Pan Y, Li Y, Yu D, Li C, Chang J, Wu S, Wang Z, Zhang X, Gu X, Weng Y. Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4520-4539. [PMID: 37201922 DOI: 10.1093/jxb/erad181] [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: 02/10/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1, and a wild-type-like mutant, lh2, in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB-CsPIF3-CsGA20ox-2-DELLA and CsPIF3-auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis.
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Affiliation(s)
- Jianyu Zhao
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
| | - Kailiang Bo
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
- College of Horticulture, Northwest A& F University, Yangling 712100, China
| | - Yuhong Li
- College of Horticulture, Northwest A& F University, Yangling 712100, China
| | - Daoliang Yu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiang Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongyi Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaolan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53705, USA
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Sharma A, Samtani H, Sahu K, Sharma AK, Khurana JP, Khurana P. Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review. Int J Biol Macromol 2023:125234. [PMID: 37290549 DOI: 10.1016/j.ijbiomac.2023.125234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.
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Affiliation(s)
- Aishwarye Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Karishma Sahu
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Jitendra Paul Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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Jia Y, Kong X, Hu K, Cao M, Liu J, Ma C, Guo S, Yuan X, Zhao S, Robert HS, Li C, Tian H, Ding Z. Corrigendum. THE NEW PHYTOLOGIST 2023; 238:2251-2252. [PMID: 37031368 DOI: 10.1111/nph.18884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
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Lee SW, Choi D, Moon H, Kim S, Kang H, Paik I, Huq E, Kim DH. PHYTOCHROME-INTERACTING FACTORS are involved in starch degradation adjustment via inhibition of the carbon metabolic regulator QUA-QUINE STARCH in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:110-123. [PMID: 36710626 DOI: 10.1111/tpj.16124] [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: 04/27/2021] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants encounter dynamic and challenging environments daily, including abiotic/biotic stresses. The regulation of carbon and nitrogen allocations for the synthesis of plant proteins, carbohydrates, and lipids is fundamental for plant growth and adaption to its surroundings. Light, one of the essential environmental signals, exerts a substantial impact on plant metabolism and resource partitioning (i.e., starch). However, it is not fully understood how light signaling affects carbohydrate production and allocation in plant growth and development. An orphan gene unique to Arabidopsis thaliana, named QUA-QUINE STARCH (QQS) is involved in the metabolic processes for partitioning of carbon and nitrogen among proteins and carbohydrates, thus influencing leaf, seed composition, and plant defense in Arabidopsis. In this study, we show that PHYTOCHROME-INTERACTING bHLH TRANSCRIPTION FACTORS (PIFs), including PIF4, are required to suppress QQS during the period at dawn, thus preventing overconsumption of starch reserves. QQS expression is significantly de-repressed in pif4 and pifQ, while repressed by overexpression of PIF4, suggesting that PIF4 and its close homologs (PIF1, PIF3, and PIF5) act as negative regulators of QQS expression. In addition, we show that the evening complex, including ELF3 is required for active expression of QQS, thus playing a positive role in starch catabolism during night-time. Furthermore, QQS is epigenetically suppressed by DNA methylation machinery, whereas histone H3 K4 methyltransferases (e.g., ATX1, ATX2, and ATXR7) and H3 acetyltransferases (e.g., HAC1 and HAC5) are involved in the expression of QQS. This study demonstrates that PIF light signaling factors help plants utilize optimal amounts of starch during the night and prevent overconsumption of starch before its biosynthesis during the upcoming day.
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sujeong Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hajeong Kang
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Inyup Paik
- Department of Molecular Biosciences, the University of Texas at Austin, Texas, 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences, the University of Texas at Austin, Texas, 78712, USA
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
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Sng BJR, Van Vu K, Choi IKY, Chin HJ, Jang IC. LONG HYPOCOTYL IN FAR-RED 1 mediates a trade-off between growth and defense under shade in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad088. [PMID: 36882154 DOI: 10.1093/jxb/erad088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 06/18/2023]
Abstract
Plants respond to vegetative shade with developmental and physiological changes that is collectively known as shade avoidance syndrome (SAS). Although LONG HYPOCOTYL IN FAR-RED 1 (HFR1) is known to be a negative regulator of SAS by forming heterodimers with other basic helix-loop-helix (bHLH) transcription factors to inhibit them, its function in genome-wide transcriptional regulation is not fully elucidated. Here, we performed RNA-sequencing analyses of hfr1-5 and HFR1 overexpression line (HFR1(ΔN)-OE) to comprehensively identify HFR1-regulated genes at different time points of shade treatment. We found that HFR1 mediates the trade-off between shade-induced growth and shade-repressed defense, by regulating the expression of relevant genes in shade. Genes involved in promoting growth, such as for auxin biosynthesis, transport, signaling and response were induced by shade but suppressed by HFR1 at both short and long durations of shade. Likewise, most ethylene-related genes were shade-induced and HFR1-repressed. On the other hand, shade suppressed defense-related genes while HFR1 induced their expression, especially under long duration of shade treatment. We demonstrated that HFR1 confers increased resistance to bacterial infection under shade.
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Affiliation(s)
- Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Kien Van Vu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Ian Kin Yuen Choi
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Hui Jun Chin
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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Xu P, Jinbo H, Cai W. Karrikin signaling regulates hypocotyl shade avoidance response by modulating auxin homeostasis in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:1748-1761. [PMID: 36068957 DOI: 10.1111/nph.18459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Shade affects all aspects of plant growth and development, including seed germination, hypocotyl elongation, petiole growth, leaf hyponasty, and flowering time. Here, we found that mutations in the key Arabidopsis karrikins signal perception-associated KARRIKIN INSENSITIVE 2 (KAI2) gene, encoding an α/β-fold hydrolase, and the MORE AXILLARY GROWTH 2 (MAX2) gene, encoding an F-box protein, led to greater hypocotyl elongation under shade avoidance conditions. We further verified that these phenotypes were caused by perception of the endogenous KAI2-ligands (KLs), and that this phenotype is independent of strigolactone biosynthetic or signaling pathways. Upon perception of a KL, it is probable that the target protein forms a complex with the KAI2/MAX2 proteins, which are degraded through the action of the 26S proteasome. We demonstrated that SUPPRESSOR OF MAX2-1 (SMAX1) is the degradation target for the KAI2/MAX2 complex in the context of shade avoidance. KAI2 and MAX2 require SMAX1 to limit the hypocotyl growth associated with shade avoidance. Treatment with l-kynurenine, an inhibitor of auxin accumulation, partially restored elongation of kai2 mutant hypocotyls under simulated shade. Furthermore, KAI2 is involved in regulating auxin accumulation and polar auxin transport, which may contribute to the hypocotyl shade response. In addition, SMAX1 gene overexpression promoted the hypocotyl shade response. RNA-sequencing analysis revealed that SMAX1-overexpression affected the expression of many auxin homeostasis genes, especially under simulated shade. Altogether, our data support the conclusion that KL signaling regulates shade avoidance by modulating auxin homeostasis in the hypocotyl.
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Affiliation(s)
- Peipei Xu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hu Jinbo
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Weiming Cai
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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10
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Luo F, Zhang Q, Xin H, Liu H, Yang H, Doblin MS, Bacic A, Li L. A Phytochrome B-PIF4-MYC2/MYC4 module inhibits secondary cell wall thickening in response to shaded light. PLANT COMMUNICATIONS 2022; 3:100416. [PMID: 35927944 PMCID: PMC9700123 DOI: 10.1016/j.xplc.2022.100416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 06/01/2023]
Abstract
Secondary cell walls (SCWs) in stem cells provide mechanical strength and structural support for growth. SCW thickening varies under different light conditions. Our previous study revealed that blue light enhances SCW thickening through the redundant function of MYC2 and MYC4 directed by CRYPTOCHROME1 (CRY1) signaling in fiber cells of the Arabidopsis inflorescence stem. In this study, we find that the Arabidopsis PHYTOCHROME B mutant phyB displays thinner SCWs in stem fibers, but thicker SCWs are deposited in the PHYTOCHROME INTERACTING FACTOR (PIF) quadruple mutant pif1pif3pif4pif5 (pifq). The shaded light condition with a low ratio of red to far-red light inhibits stem SCW thickening. PIF4 interacts with MYC2 and MYC4 to affect their localization in nuclei, and this interaction results in inhibition of the MYCs' transactivation activity on the NST1 promoter. Genetic evidence shows that regulation of SCW thickening by PIFs is dependent on MYC2/MYC4 function. Together, the results of this study reveal a PHYB-PIF4-MYC2/MYC4 module that inhibits SCW thickening in fiber cells of the Arabidopsis stem.
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Affiliation(s)
- Fang Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Xin
- Key Laboratory of Biodiversity Conservation in Southwest, State Forestry Administration, Southwest Forestry University, Kunming 650224, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongquan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Monika S Doblin
- La Trobe Institute for Agriculture and Food, School of Agriculture, Biomedicine and Environment, Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC 3086, Australia; Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Antony Bacic
- La Trobe Institute for Agriculture and Food, School of Agriculture, Biomedicine and Environment, Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC 3086, Australia; Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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11
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Zhao J, Shi X, Chen L, Chen Q, Tian X, Ai L, Zhao H, Yang C, Yan L, Zhang M. Genetic and transcriptome analyses reveal the candidate genes and pathways involved in the inactive shade-avoidance response enabling high-density planting of soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:973643. [PMID: 35991396 PMCID: PMC9382032 DOI: 10.3389/fpls.2022.973643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
High-density planting is a major way to improve crop yields. However, shade-avoidance syndrome (SAS) is a major factor limiting increased planting density. First Green Revolution addressed grass lodging problem by using dwarf/semi-dwarf genes. However, it is not suitable for soybean, which bear seeds on stalk and whose seed yield depends on plant height. Hence, mining shade-tolerant germplasms and elucidating the underlying mechanism could provide meaningful resources and information for high-yield breeding. Here, we report a high-plant density-tolerant soybean cultivar, JiDou 17, which exhibited an inactive SAS (iSAS) phenotype under high-plant density or low-light conditions at the seedling stage. A quantitative trait locus (QTL) mapping analysis using a recombinant inbred line (RIL) population showed that this iSAS phenotype is related to a major QTL, named shade-avoidance response 1 (qSAR1), which was detected. The mapping region was narrowed by a haplotype analysis into a 554 kb interval harboring 44 genes, including 4 known to be key regulators of the SAS network and 4 with a variance response to low-light conditions between near isogenic line (NIL) stems. Via RNA-seq, we identified iSAS-specific genes based on one pair of near isogenic lines (NILs) and their parents. The iSAS-specific genes expressed in the stems were significantly enriched in the "proteasomal protein catabolic" process and the proteasome pathway, which were recently suggested to promote the shade-avoidance response by enhancing PIF7 stability. Most iSAS-specific proteasome-related genes were downregulated under low-light conditions. The expression of genes related to ABA, CK, and GA significantly varied between the low- and normal-light conditions. This finding is meaningful for the cloning of genes that harbor beneficial variation(s) conferring the iSAS phenotype fixed in domestication and breeding practice.
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Affiliation(s)
- Jing Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- School of Life Sciences, Yantai University, Yantai, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Lei Chen
- School of Life Sciences, Yantai University, Yantai, China
| | - Qiang Chen
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xuan Tian
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Lijuan Ai
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Hongtao Zhao
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
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12
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Abstract
AGAMOUS-LIKE 24 (AGL24) is a key gene regulating floral transition, but its involvement in flower organ identity remains largely unknown. In this study, we found that RhAGL24 is strongly related to petal and stamen development in rose. Its expression increases rapidly at the petal primordium development stage and maintains a high level until the complete differentiation stage. RhAGL24 silencing increases the number of malformed petals and decreases the number of stamens, indicating that this gene affects stamen petaloidy. RhAG (AGAMOUS), a class C gene associated with petal and stamen development, is downregulated in RhAGL24-silenced plants. Moreover, we found that RhAGL24 could directly bind to the promoter region of RhARF18 (AUXIN RESPONSE FACTORS 18), a regulator of RhAG. Our results suggested that RhAGL24-RhARF18 module regulates stamen petaloidy in rose and provide new insights into the function of AGL24 for plants.
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13
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Integration of Light and Auxin Signaling in Shade Plants: From Mechanisms to Opportunities in Urban Agriculture. Int J Mol Sci 2022; 23:ijms23073422. [PMID: 35408782 PMCID: PMC8998421 DOI: 10.3390/ijms23073422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
With intensification of urbanization throughout the world, food security is being threatened by the population surge, frequent occurrence of extreme climate events, limited area of available cultivated land, insufficient utilization of urban space, and other factors. Determining the means by which high-yielding and high-quality crops can be produced in a limited space is an urgent priority for plant scientists. Dense planting, vertical production, and indoor cultivation are effective ways to make full use of space and improve the crop yield. The results of physiological and molecular analyses of the model plant species Arabidopsis thaliana have shown that the plant response to shade is the key to regulating the plant response to changes in light intensity and quality by integrating light and auxin signals. In this study, we have summarized the major molecular mechanisms of shade avoidance and shade tolerance in plants. In addition, the biotechnological strategies of enhancing plant shade tolerance are discussed. More importantly, cultivating crop varieties with strong shade tolerance could provide effective strategies for dense planting, vertical production, and indoor cultivation in urban agriculture in the future.
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14
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Lv B, Zhu J, Kong X, Ding Z. Light participates in the auxin-dependent regulation of plant growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:819-822. [PMID: 33215867 DOI: 10.1111/jipb.13036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Light is the energy source for plant photosynthesis and influences plant growth and development. Through multiple photoreceptors, plant interprets light signals through various downstream phytohormones such as auxin. Recently, Chen et al. (2020) uncover a new layer of regulation in IPyA pathway of auxin biosynthesis by light. Here we highlight recent studies about how light controls plant growth through regulating auxin biosynthesis and signaling.
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Affiliation(s)
- Bingsheng Lv
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jiayong Zhu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xiangpei Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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15
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Li W, Liu Y, Wang W, Liu J, Yao M, Guan M, Guan C, He X. Phytochrome-interacting factor (PIF) in rapeseed (Brassica napus L.): Genome-wide identification, evolution and expression analyses during abiotic stress, light quality and vernalization. Int J Biol Macromol 2021; 180:14-27. [PMID: 33722620 DOI: 10.1016/j.ijbiomac.2021.03.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Phytochrome-interacting factors (PIFs) are members of basic helix-loop-helix (bHLH) transcription factors and the primary partners of phytochromes (PHY) in light signaling. PIFs interact with the Pfr forms of phytochrome to play an important role in the pathways of response to light and temperature in plants. In this study, 30, 12, and 16 potential PIF genes were identified in Brassica napus, Brassica rapa, Brassica oleracea, respectively, which could be divided into three subgroups. The Br/Bo/BnaPIF genes are intron-rich and similar to the PIF genes in Arabidopsis. However, unlike the AtPIFs that exist in multiple alternative-splicing forms, the majority of Br/Bo/BnaPIF genes have no alternative-splicing forms. A total of 52 Br/Bo/BnaPIF proteins have both the conserved active PHYB binding (APB) and bHLH domains. The Ka/Ks ratio revealed that most BnaPIFs underwent purifying selection. A promoter analysis found that light-related, abscisic acid-related and MYB-binding sites were the most abundant in the promoters of BnaPIFs. BnaPIF genes displayed different spatiotemporal patterns of expression and were regulated by light quality, circadian rhythms, cold, heat, and vernalization. Our results are useful for understanding the biological functions of PIF proteins in rapeseed.
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Affiliation(s)
- Wenqian Li
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yan Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Weiping Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Juncen Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mingyao Yao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mei Guan
- Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Xin He
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China.
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16
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Pierik R, Ballaré CL. Control of Plant Growth and Defense by Photoreceptors: From Mechanisms to Opportunities in Agriculture. MOLECULAR PLANT 2021; 14:61-76. [PMID: 33276158 DOI: 10.1016/j.molp.2020.11.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Plants detect and respond to the proximity of competitors using light signals perceived by photoreceptor proteins. A low ratio of red to far-red radiation (R:FR ratio) is a key signal of competition that is sensed by the photoreceptor phytochrome B (phyB). Low R:FR ratios increase the synthesis of growth-related hormones, including auxin and gibberellins, promoting stem elongation and other shade-avoidance responses. Other photoreceptors that help plants to optimize their developmental configuration and resource allocation patterns in the canopy include blue light photoreceptors, such as cryptochromes and phototropins, and UV receptors, such as UVR8. All photoreceptors act by directly or indirectly controlling the activity of two major regulatory nodes for growth and development: the COP1/SPA ubiquitin E3 ligase complex and the PIF transcription factors. phyB is also an important modulator of hormonal pathways that regulate plant defense against herbivores and pathogens, including the jasmonic acid signaling pathway. In this Perspective, we discuss recent advances on the studies of the mechanisms that link photoreceptors with growth and defense. Understanding these mechanisms is important to provide a functional platform for breeding programs aimed at improving plant productivity, stress tolerance, and crop health in species of agronomic interest, and to manipulate the light environments in protected agriculture.
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Affiliation(s)
- Ronald Pierik
- Plant Ecophysiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands.
| | - Carlos L Ballaré
- IFEVA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Ave. San Martín 4453, C1417DSE, Buenos Aires, Argentina; IIBIO-INTECH, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de San Martín, B1650HMP, Buenos Aires, Argentina.
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17
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Yang Y, Guang Y, Wang F, Chen Y, Yang W, Xiao X, Luo S, Zhou Y. Characterization of Phytochrome-Interacting Factor Genes in Pepper and Functional Analysis of CaPIF8 in Cold and Salt Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:746517. [PMID: 34759940 PMCID: PMC8572859 DOI: 10.3389/fpls.2021.746517] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/04/2021] [Indexed: 05/17/2023]
Abstract
As a subfamily of basic helix-loop-helix (bHLH) transcription factors, phytochrome-interacting factors (PIFs) participate in regulating light-dependent growth and development of plants. However, limited information is available about PIFs in pepper. In the present study, we identified six pepper PIF genes using bioinformatics-based methods. Phylogenetic analysis revealed that the PIFs from pepper and some other plants could be divided into three distinct groups. Motif analysis revealed the presence of many conserved motifs, which is consistent with the classification of PIF proteins. Gene structure analysis suggested that the CaPIF genes have five to seven introns, exhibiting a relatively more stable intron number than other plants such as rice, maize, and tomato. Expression analysis showed that CaPIF8 was up-regulated by cold and salt treatments. CaPIF8-silenced pepper plants obtained by virus-induced gene silencing (VIGS) exhibited higher sensitivity to cold and salt stress, with an obvious increase in relative electrolyte leakage (REL) and variations in the expression of stress-related genes. Further stress tolerance assays revealed that CaPIF8 plays different regulatory roles in cold and salt stress response by promoting the expression of the CBF1 gene and ABA biosynthesis genes, respectively. Our results reveal the key roles of CaPIF8 in cold and salt tolerance of pepper, and lay a solid foundation for clarifying the biological roles of PIFs in pepper and other plants.
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Affiliation(s)
- Youxin Yang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yelan Guang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Feng Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yue Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Wenting Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Xufeng Xiao
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Sha Luo
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yong Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Yong Zhou,
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18
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Zhu C, Zhang S, Zhou C, Chen L, Zaripov T, Zhan D, Weng J, Lin Y, Lai Z, Guo Y. Integrated Transcriptome, microRNA, and Phytochemical Analyses Reveal Roles of Phytohormone Signal Transduction and ABC Transporters in Flavor Formation of Oolong Tea ( Camellia sinensis) during Solar Withering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12749-12767. [PMID: 33112139 DOI: 10.1021/acs.jafc.0c05750] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The unique aroma and flavor of oolong tea develop during the withering stage of postharvest processing. We explored the roles of miRNA-related regulatory networks during tea withering and their effects on oolong tea quality. We conducted transcriptome and miRNA analyses to identify differentially expressed (DE) miRNAs and target genes among fresh leaves, indoor-withered leaves, and solar-withered leaves. We identified 32 DE-miRNAs and 41 target genes involved in phytohormone signal transduction and ABC transporters. Further analyses indicated that these two pathways regulated the accumulation of flavor-related metabolites during tea withering. Flavonoid accumulation was correlated with the miR167d_1-ARF-GH3, miR845-ABCC1-3/ABCC2, miR166d-5p_1-ABCC1-2, and miR319c_3-PIF-ARF modules. Terpenoid content was correlated with the miR171b-3p_2-DELLA-MYC2 and miR166d-5p_1-ABCG2-MYC2 modules. These modules inhibited flavonoid biosynthesis and enhanced terpenoid biosynthesis in solar-withered leaves. Low auxin and gibberellic acid contents and circRNA-related regulatory networks also regulated the accumulation of flavor compounds in solar-withered leaves. Our analyses reveal how solar withering produces high-quality oolong tea.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Timur Zaripov
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Zhan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingjing Weng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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19
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Li T, Li B, Wang L, Xie Z, Wang X, Zou L, Zhang D, Lin H. Phytochrome-interacting factor 4 (PIF4) inhibits expression of SHORT HYPOCOTYL 2 (SHY2) to promote hypocotyl growth during shade avoidance in Arabidopsis. Biochem Biophys Res Commun 2020; 534:857-863. [PMID: 33153717 DOI: 10.1016/j.bbrc.2020.10.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 11/28/2022]
Abstract
Plants sense the presence of competing neighboring vegetation as a change in light quality. These changes initiate shade avoidance syndrome (SAS) responses. PHYTOCHROME INTERACTING FACTORS (PIFs) are crucial factors in the SAS response. In particular, they mediate the expression of multiple phytohormones and cell expansion genes. Many positive regulatory factors in the SAS response have been identified, but the negative regulation of SAS transcription factors remains poorly understood. The functions of the short hypocotyl 2 (SHY2) transcription factor during the SAS response have not been established, although its roles in the participating hormone and stress responses are well documented. Here, the SHY2 loss-of-function (shy2-31) mutant had a longer hypocotyl, but the gain-of-function (shy2-2) hypocotyl was shorter than that of the wild type under white and shade conditions. We showed that the SHY2 expression level and its associated protein significantly accumulated under shade conditions. Furthermore, SHY2 transcript levels significantly increased in mutant pifQ, but decreased in PIF4OX compared to the wild type, which indicated that PIF4 is a transcriptional repressor of SHY2. ChIP assays have consistently shown that PIF4 directly binds to the promoters of SHY2. We further show that PIF4OX partially rescued the short hypocotyl characteristic of shy2-2 under white and shade conditions. Our results provide new insights into the regulatory mechanisms controlling SAS mediated elongation of the hypocotyl by PIF4-SHY2 modules in Arabidopsis.
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Affiliation(s)
- Taotao Li
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Bingbing Li
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Lianzhe Wang
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Zhaohui Xie
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Xiaotao Wang
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Lijuan Zou
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, China
| | - Dawei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
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