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Rabeh K, Oubohssaine M, Hnini M. TOR in plants: Multidimensional regulators of plant growth and signaling pathways. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154186. [PMID: 38330538 DOI: 10.1016/j.jplph.2024.154186] [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: 09/01/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Target Of Rapamycin (TOR) represents a ubiquitous kinase complex that has emerged as a central regulator of cell growth and metabolism in nearly all eukaryotic organisms. TOR is an evolutionarily conserved protein kinase, functioning as a central signaling hub that integrates diverse internal and external cues to regulate a multitude of biological processes. These processes collectively exert significant influence on plant growth, development, nutrient assimilation, photosynthesis, fruit ripening, and interactions with microorganisms. Within the plant domain, the TOR complex comprises three integral components: TOR, RAPTOR, and LST8. This comprehensive review provides insights into various facets of the TOR protein, encompassing its origin, structure, function, and the regulatory and signaling pathways operative in photosynthetic organisms. Additionally, we explore future perspectives related to this pivotal protein kinase.
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Affiliation(s)
- Karim Rabeh
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco.
| | - Malika Oubohssaine
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Mohamed Hnini
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Siodmak A, Martinez-Seidel F, Rayapuram N, Bazin J, Alhoraibi H, Gentry-Torfer D, Tabassum N, Sheikh AH, Kise J, Blilou I, Crespi M, Kopka J, Hirt H. Dynamics of ribosome composition and ribosomal protein phosphorylation in immune signaling in Arabidopsis thaliana. Nucleic Acids Res 2023; 51:11876-11892. [PMID: 37823590 PMCID: PMC10681734 DOI: 10.1093/nar/gkad827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
In plants, the detection of microbe-associated molecular patterns (MAMPs) induces primary innate immunity by the activation of mitogen-activated protein kinases (MAPKs). We show here that the MAMP-activated MAPK MPK6 not only modulates defense through transcriptional regulation but also via the ribosomal protein translation machinery. To understand the effects of MPK6 on ribosomes and their constituent ribosomal proteins (RPs), polysomes, monosomes and the phosphorylation status of the RPs, MAMP-treated WT and mpk6 mutant plants were analysed. MAMP-activation induced rapid changes in RP composition of monosomes, polysomes and in the 60S ribosomal subunit in an MPK6-specific manner. Phosphoproteome analysis showed that MAMP-activation of MPK6 regulates the phosphorylation status of the P-stalk ribosomal proteins by phosphorylation of RPP0 and the concomitant dephosphorylation of RPP1 and RPP2. These events coincide with a significant decrease in the abundance of ribosome-bound RPP0s, RPP1s and RPP3s in polysomes. The P-stalk is essential in regulating protein translation by recruiting elongation factors. Accordingly, we found that RPP0C mutant plants are compromised in basal resistance to Pseudomonas syringae infection. These data suggest that MAMP-induced defense also involves MPK6-induced regulation of P-stalk proteins, highlighting a new role of ribosomal regulation in plant innate immunity.
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Affiliation(s)
- Anna Siodmak
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Naganand Rayapuram
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Hanna Alhoraibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21551 Jeddah, Saudi Arabia
| | - Dione Gentry-Torfer
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Naheed Tabassum
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Arsheed H Sheikh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - José Kenyi González Kise
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ikram Blilou
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
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Guo W, Luo H, Cao Y, Jiang Z, Liu H, Zou J, Sheng C, Xi Y. Multi-omics research on common allergens during the ripening of pollen and poplar flocs of Populus deltoides. FRONTIERS IN PLANT SCIENCE 2023; 14:1136613. [PMID: 37396639 PMCID: PMC10313134 DOI: 10.3389/fpls.2023.1136613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/23/2023] [Indexed: 07/04/2023]
Abstract
Background Populus deltoides is widely cultivated in China and produces a large number of pollen and poplar flocs from March to June per year. Previous studies have found that the pollen of P. deltoides contains allergens. However, studies on the ripening mechanism of pollen/poplar flocs and their common allergens are very limited. Methods Proteomics and metabolomics were used to study the changes of proteins and metabolites in pollen and poplar flocs of P. deltoides at different developmental stages. Allergenonline database was used to identify common allergens in pollen and poplar flocs at different developmental stages. Western blot (WB) was used to detect the biological activity of common allergens between mature pollen and poplar flocs. Results In total, 1400 differently expressed proteins (DEPs) and 459 different metabolites (DMs) were identified from pollen and poplar flocs at different developmental stages. KEGG enrichment analysis showed that DEPs in pollen and poplar flocs were significantly enriched in ribosome and oxidative phosphorylation signaling pathways. The DMs in pollen are mainly involved in aminoacyl-tRNA biosynthesis and arginine biosynthesis, while the DMs in poplar flocs are mainly involved in glyoxylate and dicarboxylate metabolism. Additionally, 72 common allergens were identified in pollen and poplar flocs at different developmental stages. WB showed that there were distinct binding bands between 70 and 17KD at the two groups of allergens. Conclusions A multitude of proteins and metabolites are closely related to the ripening of pollen and poplar flocs of Populus deltoides, and they contain common allergens between mature pollen and poplar flocs.
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Affiliation(s)
- Wei Guo
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Hui Luo
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Yi Cao
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Ziyun Jiang
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Hui Liu
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Jie Zou
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Changle Sheng
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Yilong Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
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Yue K, Lingling L, Xie J, Coulter JA, Luo Z. Synthesis and regulation of auxin and abscisic acid in maize. PLANT SIGNALING & BEHAVIOR 2021; 16:1891756. [PMID: 34057034 PMCID: PMC8205056 DOI: 10.1080/15592324.2021.1891756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Indole-3-acetic acid (IAA), the primary auxin in higher plants, and abscisic acid (ABA) play crucial roles in the ability of maize (Zea mays L.) to acclimatize to various environments by mediating growth, development, defense and nutrient allocation. Although understanding the biochemical reactions for IAA and ABA biosynthesis and signal transduction has progressed, the mechanisms by which auxin and ABA are synthesized and transduced in maize have not been fully elucidated to date. The synthesis and signal transduction pathway of IAA and ABA in maize can be analyzed using an existing model. This article focuses on the research progress toward understanding the synthesis and signaling pathways of IAA and ABA, as well as IAA and ABA regulation of maize growth, providing insight for future development and the significance of IAA and ABA for maize improvement.
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Affiliation(s)
- Kai Yue
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Li Lingling
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- CONTACT Lingling Li College of Agronomy/Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Junhong Xie
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jeffrey A. Coulter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Zhuzhu Luo
- College of Resource and Environment, Gansu Agricultural University, Lanzhou, China
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Uzair M, Long H, Zafar SA, Patil SB, Chun Y, Li L, Fang J, Zhao J, Peng L, Yuan S, Li X. Narrow Leaf21, encoding ribosomal protein RPS3A, controls leaf development in rice. PLANT PHYSIOLOGY 2021; 186:497-518. [PMID: 33591317 PMCID: PMC8154097 DOI: 10.1093/plphys/kiab075] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 05/19/2023]
Abstract
Leaf morphology influences photosynthesis, transpiration, and ultimately crop yield. However, the molecular mechanism of leaf development is still not fully understood. Here, we identified and characterized the narrow leaf21 (nal21) mutant in rice (Oryza sativa), showing a significant reduction in leaf width, leaf length and plant height, and increased tiller number. Microscopic observation revealed defects in the vascular system and reduced epidermal cell size and number in the nal21 leaf blade. Map-based cloning revealed that NAL21 encodes a ribosomal small subunit protein RPS3A. Ribosome-targeting antibiotics resistance assay and ribosome profiling showed a significant reduction in the free 40S ribosome subunit in the nal21 mutant. The nal21 mutant showed aberrant auxin responses in which multiple auxin response factors (ARFs) harboring upstream open-reading frames (uORFs) in their 5'-untranslated region were repressed at the translational level. The WUSCHEL-related homeobox 3A (OsWOX3A) gene, a key transcription factor involved in leaf blade lateral outgrowth, is also under the translational regulation by RPS3A. Transformation with modified OsARF11, OsARF16, and OsWOX3A genomic DNA (gDNA) lacking uORFs rescued the narrow leaf phenotype of nal21 to a better extent than transformation with their native gDNA, implying that RPS3A could regulate translation of ARFs and WOX3A through uORFs. Our results demonstrate that proper translational regulation of key factors involved in leaf development is essential to maintain normal leaf morphology.
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Affiliation(s)
- Muhammad Uzair
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haixin Long
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Syed Adeel Zafar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suyash B Patil
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixiang Peng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Author for communication:
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Li K, Zhou X, Sun X, Li G, Hou L, Zhao S, Zhao C, Ma C, Li P, Wang X. Coordination between MIDASIN 1-mediated ribosome biogenesis and auxin modulates plant development. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2501-2513. [PMID: 33476386 DOI: 10.1093/jxb/erab025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Ribosomes are required for plant growth and development, and ribosome biogenesis-deficient mutants generally display auxin-related phenotypes. Although the relationship between ribosome dysfunction and auxin is known, many aspects of this subject remain to be understood. We previously reported that MIDASIN 1 (MDN1) is an essential pre-60S ribosome biogenesis factor (RBF) in Arabidopsis. In this study, we further characterized the aberrant auxin-related phenotypes of mdn1-1, a weak mutant allele of MDN1. Auxin response is disturbed in both shoots and roots of mdn1-1, as indicated by the DR5:GUS reporter. By combining transcriptome profiling analysis and reporter gene detection, we found that expression of genes involved in auxin biosynthesis, transport, and signaling is changed in mdn1-1. Furthermore, MDN1 deficiency affects the post-transcriptional regulation and protein distribution of PIN-FORMED 2 (PIN2, an auxin efflux facilitator) in mdn1-1 roots. These results indicate that MDN1 is required for maintaining the auxin system. More interestingly, MDN1 is an auxin-responsive gene, and its promoter can be targeted by multiple AUXIN RESPONSE FACTORs (ARFs), including ARF7 and ARF19, in vitro. Indeed, in arf7 arf19, the auxin sensitivity of MDN1 expression is significantly reduced. Together, our results reveal a coordination mechanism between auxin and MDN1-dependent ribosome biogenesis for regulating plant development.
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Affiliation(s)
- Ke Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
- College of Life Science, Shandong University, Qingdao 266237, PR China
| | - Ximeng Zhou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Xueping Sun
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Guanghui Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
- College of Life Science, Shandong University, Qingdao 266237, PR China
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
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Obomighie I, Lapenas K, Murphy BE, Bowles AMC, Bechtold U, Prischi F. The Role of Ribosomal Protein S6 Kinases in Plant Homeostasis. Front Mol Biosci 2021; 8:636560. [PMID: 33778006 PMCID: PMC7988200 DOI: 10.3389/fmolb.2021.636560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/11/2021] [Indexed: 01/11/2023] Open
Abstract
The p70 ribosomal S6 kinase (S6K) family is a group of highly conserved kinases in eukaryotes that regulates cell growth, cell proliferation, and stress response via modulating protein synthesis and ribosomal biogenesis. S6Ks are downstream effectors of the Target of Rapamycin (TOR) pathway, which connects nutrient and energy signaling to growth and homeostasis, under normal and stress conditions. The plant S6K family includes two isoforms, S6K1 and S6K2, which, despite their high level of sequence similarity, have distinct functions and regulation mechanisms. Significant advances on the characterization of human S6Ks have occurred in the past few years, while studies on plant S6Ks are scarce. In this article, we review expression and activation of the two S6K isoforms in plants and we discuss their roles in mediating responses to stresses and developmental cues.
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Affiliation(s)
| | - Kestutis Lapenas
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Billy E Murphy
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Ulrike Bechtold
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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González-López O, Palacios-Nava BB, Peña-Uribe CA, Campos-García J, López-Bucio J, García-Pineda E, Reyes de la Cruz H. Growth promotion in Arabidopsis thaliana by bacterial cyclodipeptides involves the TOR/S6K pathway activation. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153343. [PMID: 33387853 DOI: 10.1016/j.jplph.2020.153343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Cyclodipeptides (CDPs) are the smallest peptidic molecules that can be produced by diverse organisms such as bacteria, fungi, and animals. They have multiple biological effects. In this paper, we examined the CDPs produced by the bacteria Pseudomonas aeruginosa PAO1, which are known as opportunistic pathogens of humans and plants on TARGET OF RAPAMYCIN (TOR) signaling pathways, and regulation of root system architecture. This bacterium produces the bioactive CDPs: cyclo(L-Pro-L-Leu), cyclo(L-Pro-L-Phe), cyclo(L-Pro-L-Tyr), and cyclo(L-Pro-L-Val). In a previous report, these molecules were found to modulate basic cellular programs not only via auxin mechanisms but also by promoting the phosphorylation of the S6 ribosomal protein kinase (S6K), a downstream substrate of the TOR kinase. In the present work, we found that the inoculation of Arabidopsis plants with P. aeruginosa PAO1, the non-pathogenic P. aeruginosa ΔlasI/Δrhll strain (JM2), or by direct exposure of plants to CDPs influenced growth and promoted root branching depending upon the treatment imposed, while genetic evidence using Arabidopsis lines with enhanced or decreased TOR levels indicated a critical role of this pathway in the bacterial phytostimulation.
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Affiliation(s)
- Omar González-López
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico
| | - Brenda Berenice Palacios-Nava
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico
| | - César Arturo Peña-Uribe
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico
| | - Jesús Campos-García
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico
| | - Ernesto García-Pineda
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico
| | - Homero Reyes de la Cruz
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ed B1, B3, A1', U3, Ciudad Universitaria, Morelia, Michoacán, CP 58030, Mexico.
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Wang P, Wang T, Han J, Li M, Zhao Y, Su T, Ma C. Plant Autophagy: An Intricate Process Controlled by Various Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:754982. [PMID: 34630498 PMCID: PMC8495024 DOI: 10.3389/fpls.2021.754982] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/31/2021] [Indexed: 05/17/2023]
Abstract
Autophagy is a ubiquitous process used widely across plant cells to degrade cellular material and is an important regulator of plant growth and various environmental stress responses in plants. The initiation and dynamics of autophagy in plant cells are precisely controlled according to the developmental stage of the plant and changes in the environment, which are transduced into intracellular signaling pathways. These signaling pathways often regulate autophagy by mediating TOR (Target of Rapamycin) kinase activity, an important regulator of autophagy initiation; however, some also act via TOR-independent pathways. Under nutrient starvation, TOR activity is suppressed through glucose or ROS (reactive oxygen species) signaling, thereby promoting the initiation of autophagy. Under stresses, autophagy can be regulated by the regulatory networks connecting stresses, ROS and plant hormones, and in turn, autophagy regulates ROS levels and hormone signaling. This review focuses on the latest research progress in the mechanism of different external signals regulating autophagy.
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10
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Mugume Y, Kazibwe Z, Bassham DC. Target of Rapamycin in Control of Autophagy: Puppet Master and Signal Integrator. Int J Mol Sci 2020; 21:ijms21218259. [PMID: 33158137 PMCID: PMC7672647 DOI: 10.3390/ijms21218259] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
The target of rapamycin (TOR) is an evolutionarily-conserved serine/threonine kinase that senses and integrates signals from the environment to coordinate developmental and metabolic processes. TOR senses nutrients, hormones, metabolites, and stress signals to promote cell and organ growth when conditions are favorable. However, TOR is inhibited when conditions are unfavorable, promoting catabolic processes such as autophagy. Autophagy is a macromolecular degradation pathway by which cells degrade and recycle cytoplasmic materials. TOR negatively regulates autophagy through phosphorylation of ATG13, preventing activation of the autophagy-initiating ATG1-ATG13 kinase complex. Here we review TOR complex composition and function in photosynthetic and non-photosynthetic organisms. We also review recent developments in the identification of upstream TOR activators and downstream effectors of TOR. Finally, we discuss recent developments in our understanding of the regulation of autophagy by TOR in photosynthetic organisms.
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11
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Scarpin MR, Leiboff S, Brunkard JO. Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation. eLife 2020; 9:e58795. [PMID: 33054972 PMCID: PMC7584452 DOI: 10.7554/elife.58795] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.
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Affiliation(s)
- M Regina Scarpin
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
| | - Samuel Leiboff
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Laboratory of Genetics, University of Wisconsin—MadisonMadisonUnited States
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12
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Jamsheer K M, Jindal S, Laxmi A. Evolution of TOR-SnRK dynamics in green plants and its integration with phytohormone signaling networks. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2239-2259. [PMID: 30870564 DOI: 10.1093/jxb/erz107] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/26/2019] [Indexed: 05/07/2023]
Abstract
The target of rapamycin (TOR)-sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) signaling is an ancient regulatory mechanism that originated in eukaryotes to regulate nutrient-dependent growth. Although the TOR-SnRK1 signaling cascade shows highly conserved functions among eukaryotes, studies in the past two decades have identified many important plant-specific innovations in this pathway. Plants also possess SnRK2 and SnRK3 kinases, which originated from the ancient SnRK1-related kinases and have specialized roles in controlling growth, stress responses and nutrient homeostasis in plants. Recently, an integrative picture has started to emerge in which different SnRKs and TOR kinase are highly interconnected to control nutrient and stress responses of plants. Further, these kinases are intimately involved with phytohormone signaling networks that originated at different stages of plant evolution. In this review, we highlight the evolution and divergence of TOR-SnRK signaling components in plants and their communication with each other as well as phytohormone signaling to fine-tune growth and stress responses in plants.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Noida, India
| | - Sunita Jindal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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13
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Gupta R, Min CW, Meng Q, Agrawal GK, Rakwal R, Kim ST. Comparative phosphoproteome analysis upon ethylene and abscisic acid treatment in Glycine max leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:173-180. [PMID: 29990770 DOI: 10.1016/j.plaphy.2018.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 05/06/2023]
Abstract
Abscisic acid (ABA) and ethylene play key roles in growth and development of plants. Several attempts have been made to investigate the ABA and ethylene-induced signaling in plants, however, the involvement of phosphorylation and dephosphorylation in fine-tuning of the induced response has not been investigated much. Here, a phosphoproteomic analysis was carried out to identify the phosphoproteins in response to ABA, ethylene (ET) and combined ABA + ET treatments in soybean leaves. Phosphoproteome analysis led to the identification of 802 phosphopeptides, representing 422 unique protein groups. A comparative analysis led to the identification of 40 phosphosites that significantly changed in response to given hormone treatments. Functional annotation of the identified phosphoproteins showed that these were majorly involved in nucleic acid binding, signaling, transport and stress response. Localization prediction showed that 67% of the identified phosphoproteins were nuclear, indicating their potential involvement in gene regulation. Taken together, these results provide an overview of the ABA, ET and combined ABA + ET signaling in soybean leaves at phosphoproteome level.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 627-707, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 627-707, Republic of Korea
| | - Qingfeng Meng
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 627-707, Republic of Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8574, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo, 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 627-707, Republic of Korea.
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14
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Schepetilnikov M, Ryabova LA. Auxin Signaling in Regulation of Plant Translation Reinitiation. FRONTIERS IN PLANT SCIENCE 2017; 8:1014. [PMID: 28659957 PMCID: PMC5469914 DOI: 10.3389/fpls.2017.01014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/26/2017] [Indexed: 05/03/2023]
Abstract
The mRNA translation machinery directs protein production, and thus cell growth, according to prevailing cellular and environmental conditions. The target of rapamycin (TOR) signaling pathway-a major growth-related pathway-plays a pivotal role in optimizing protein synthesis in mammals, while its deregulation triggers uncontrolled cell proliferation and the development of severe diseases. In plants, several signaling pathways sensitive to environmental changes, hormones, and pathogens have been implicated in post-transcriptional control, and thus far phytohormones have attracted most attention as TOR upstream regulators in plants. Recent data have suggested that the coordinated actions of the phytohormone auxin, Rho-like small GTPases (ROPs) from plants, and TOR signaling contribute to translation regulation of mRNAs that harbor upstream open reading frames (uORFs) within their 5'-untranslated regions (5'-UTRs). This review will summarize recent advances in translational regulation of a specific set of uORF-containing mRNAs that encode regulatory proteins-transcription factors, protein kinases and other cellular controllers-and how their control can impact plant growth and development.
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Affiliation(s)
- Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de StrasbourgStrasbourg, France
| | - Lyubov A. Ryabova
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de StrasbourgStrasbourg, France
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15
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Deng K, Dong P, Wang W, Feng L, Xiong F, Wang K, Zhang S, Feng S, Wang B, Zhang J, Ren M. The TOR Pathway Is Involved in Adventitious Root Formation in Arabidopsis and Potato. FRONTIERS IN PLANT SCIENCE 2017; 8:784. [PMID: 28553309 PMCID: PMC5427086 DOI: 10.3389/fpls.2017.00784] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/26/2017] [Indexed: 05/14/2023]
Abstract
In the agriculture industry, adventitious root formation is a core issue of plants asexual propagation. However, the underlying molecular mechanism of adventitious root formation is far beyond understanding. In present study we found that target of rapamycin (TOR) signaling plays a key role in adventitious root formation in potato and Arabidopsis. The core components of TOR complex including TOR, RAPTOR, and LST8 are highly conserved in potato, but the seedlings of potato are insensitive to rapamycin, implying FK506 Binding Protein 12 KD (FKBP12) lost the function to bridge the interaction of rapamycin and TOR in potato. To dissect TOR signaling in potato, the rapamycin hypersensitive potato plants (BP12-OE) were engineered by introducing yeast FKBP12 (ScFKBP12) into potato. We found that rapamycin can significantly attenuate the capability of adventitious root formation in BP12-OE potatoes. KU63794 (KU, an active-site TOR inhibitor) combined with rapamycin can more significantly suppress adventitious root formation of BP12-OE potato than the single treatments, such as KU63794 or rapamycin, indicating its synergistic inhibitory effects on potato adventitious root formation. Furthermore, RNA-seq data showed that many genes associated with auxin signaling pathway were altered when BP12-OE potato seedlings were treated with rapamycin + KU, suggesting that TOR may play a major role in adventitious root formation via auxin signaling. The auxin receptor mutant tir1 was sensitive to TOR inhibitors and the double and quadruple mutants including tir1afb2, tir1afb3, and tir1afb1afb2afb3 displayed more sensitive to asTORis than single mutant tir1. Consistently, overexpression of AtTIR1 in Arabidopsis and potato can partially overcome the inhibitory effect of asTORis and promote adventitious root formation under asTORis treatments. These observations suggest that TOR signaling regulates adventitious root formation by mediating auxin signaling in Arabidopsis and potato.
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Affiliation(s)
- Kexuan Deng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Pan Dong
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Wanjing Wang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Li Feng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Fangjie Xiong
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Kai Wang
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Shumin Zhang
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Shun Feng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Bangjun Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Life Sciences, Southwest UniversityChongqing, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing UniversityChongqing, China
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16
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Merchante C, Stepanova AN, Alonso JM. Translation regulation in plants: an interesting past, an exciting present and a promising future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:628-653. [PMID: 28244193 DOI: 10.1111/tpj.13520] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
Abstract
Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever-changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well-established and uncharacterized translation-dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.
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Affiliation(s)
- Catharina Merchante
- Departamento de Biologia Molecular y Bioquimica, Universidad de Malaga-Instituto de Hortofruticultura Subtropical y Mediterranea, IHSM-UMA-CSIC, Malaga, Andalucía, Spain
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
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17
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Schepetilnikov M, Makarian J, Srour O, Geldreich A, Yang Z, Chicher J, Hammann P, Ryabova LA. GTPase ROP2 binds and promotes activation of target of rapamycin, TOR, in response to auxin. EMBO J 2017; 36:886-903. [PMID: 28246118 DOI: 10.15252/embj.201694816] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 01/16/2023] Open
Abstract
Target of rapamycin (TOR) promotes reinitiation at upstream ORFs (uORFs) in genes that play important roles in stem cell regulation and organogenesis in plants. Here, we report that the small GTPase ROP2, if activated by the phytohormone auxin, promotes activation of TOR, and thus translation reinitiation of uORF-containing mRNAs. Plants with high levels of active ROP2, including those expressing constitutively active ROP2 (CA-ROP2), contain high levels of active TOR ROP2 physically interacts with and, when GTP-bound, activates TOR in vitro TOR activation in response to auxin is abolished in ROP-deficient rop2 rop6 ROP4 RNAi plants. GFP-TOR can associate with endosome-like structures in ROP2-overexpressing plants, indicating that endosomes mediate ROP2 effects on TOR activation. CA-ROP2 is efficient in loading uORF-containing mRNAs onto polysomes and stimulates translation in protoplasts, and both processes are sensitive to TOR inhibitor AZD-8055. TOR inactivation abolishes ROP2 regulation of translation reinitiation, but not its effects on cytoskeleton or intracellular trafficking. These findings imply a mode of translation control whereby, as an upstream effector of TOR, ROP2 coordinates TOR function in translation reinitiation pathways in response to auxin.
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Affiliation(s)
- Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Joelle Makarian
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Ola Srour
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Angèle Geldreich
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Zhenbiao Yang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA
| | - Johana Chicher
- Plateforme Proteómique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme Proteómique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France
| | - Lyubov A Ryabova
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
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18
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Enganti R, Cho SK, Toperzer JD, Urquidi-Camacho RA, Cakir OS, Ray AP, Abraham PE, Hettich RL, von Arnim AG. Phosphorylation of Ribosomal Protein RPS6 Integrates Light Signals and Circadian Clock Signals. FRONTIERS IN PLANT SCIENCE 2017; 8:2210. [PMID: 29403507 PMCID: PMC5780430 DOI: 10.3389/fpls.2017.02210] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/15/2017] [Indexed: 05/20/2023]
Abstract
The translation of mRNA into protein is tightly regulated by the light environment as well as by the circadian clock. Although changes in translational efficiency have been well documented at the level of mRNA-ribosome loading, the underlying mechanisms are unclear. The reversible phosphorylation of RIBOSOMAL PROTEIN OF THE SMALL SUBUNIT 6 (RPS6) has been known for 40 years, but the biochemical significance of this event remains unclear to this day. Here, we confirm using a clock-deficient strain of Arabidopsis thaliana that RPS6 phosphorylation (RPS6-P) is controlled by the diel light-dark cycle with a peak during the day. Strikingly, when wild-type, clock-enabled, seedlings that have been entrained to a light-dark cycle are placed under free-running conditions, the circadian clock drives a cycle of RPS6-P with an opposite phase, peaking during the subjective night. We show that in wild-type seedlings under a light-dark cycle, the incoherent light and clock signals are integrated by the plant to cause an oscillation in RPS6-P with a reduced amplitude with a peak during the day. Sucrose can stimulate RPS6-P, as seen when sucrose in the medium masks the light response of etiolated seedlings. However, the diel cycles of RPS6-P are observed in the presence of 1% sucrose and in its absence. Sucrose at a high concentration of 3% appears to interfere with the robust integration of light and clock signals at the level of RPS6-P. Finally, we addressed whether RPS6-P occurs uniformly in polysomes, non-polysomal ribosomes and their subunits, and non-ribosomal protein. It is the polysomal RPS6 whose phosphorylation is most highly stimulated by light and repressed by darkness. These data exemplify a striking case of contrasting biochemical regulation between clock signals and light signals. Although the physiological significance of RPS6-P remains unknown, our data provide a mechanistic basis for the future understanding of this enigmatic event.
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Affiliation(s)
- Ramya Enganti
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
| | - Sung Ki Cho
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
| | - Jody D. Toperzer
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
| | - Ricardo A. Urquidi-Camacho
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
| | - Ozkan S. Cakir
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
| | - Alexandria P. Ray
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
| | - Paul E. Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Albrecht G. von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
- *Correspondence: Albrecht G. von Arnim,
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19
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Muneer S, Ko CH, Wei H, Chen Y, Jeong BR. Physiological and Proteomic Investigations to Study the Response of Tomato Graft Unions under Temperature Stress. PLoS One 2016; 11:e0157439. [PMID: 27310261 PMCID: PMC4911148 DOI: 10.1371/journal.pone.0157439] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/31/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Grafting is an established practice for asexual propagation in horticultural and agricultural crops. The study on graft unions has become of interest for horticulturists using proteomic and genomic techniques to observe transfer of genetic material and signal transduction pathways from root to shoot and shoot to root. Another reason to study the graft unions was potentially to observe resistance against abiotic stresses. Using physiological and proteomic analyses, we investigated graft unions (rootstock and scions) of tomato genotypes exposed to standard-normal (23/23 and 25/18°C day/night) and high-low temperatures (30/15°C day/night). RESULTS Graft unions had varied responses to the diverse temperatures. High-low temperature, but not standard-normal temperature, induced the production of reactive oxygen species (ROS) in the form of H2O2 and O2-1 in rootstock and scions. However, the expression of many cell protection molecules was also induced, including antioxidant enzymes and their immunoblots, which also show an increase in their activities such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX). The graft interfaces thus actively defend against stress by modifying their physiological and proteomic responses to establish a new cellular homeostasis. As a result, many proteins for cellular defense were regulated in graft unions under diverse temperature, in addition to the regulation of photosynthetic proteins, ion binding/transport proteins, and protein synthesis. Moreover, biomass, hardness, and vascular transport activity were evaluated to investigate the basic connectivity between rootstock and scions. CONCLUSIONS Our study provides physiological evidence of the grafted plants' response to diverse temperature. Most notably, our study provides novel insight into the mechanisms used to adapt the diverse temperature in graft unions (rootstock/scion).
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Affiliation(s)
- Sowbiya Muneer
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Chung Ho Ko
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Hao Wei
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Yuze Chen
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
| | - Byoung Ryong Jeong
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, 660–701, Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660–701, Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju, 660–701, Korea
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20
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Deng K, Yu L, Zheng X, Zhang K, Wang W, Dong P, Zhang J, Ren M. Target of Rapamycin Is a Key Player for Auxin Signaling Transduction in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:291. [PMID: 27014314 PMCID: PMC4786968 DOI: 10.3389/fpls.2016.00291] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/23/2016] [Indexed: 05/08/2023]
Abstract
Target of rapamycin (TOR), a master sensor for growth factors and nutrition availability in eukaryotic species, is a specific target protein of rapamycin. Rapamycin inhibits TOR kinase activity viaFK506 binding protein 12 kDa (FKBP12) in all examined heterotrophic eukaryotic organisms. In Arabidopsis, several independent studies have shown that AtFKBP12 is non-functional under aerobic condition, but one study suggests that AtFKBP12 is functional during anaerobic growth. However, the functions of AtFKBP12 have never been examined in parallel under aerobic and anaerobic growth conditions so far. To this end, we cloned the FKBP12 gene of humans, yeast, and Arabidopsis, respectively. Transgenic plants were generated, and pharmacological examinations were performed in parallel with Arabidopsis under aerobic and anaerobic conditions. ScFKBP12 conferred plants with the strongest sensitivity to rapamycin, followed by HsFKBP12, whereas AtFKBP12 failed to generate rapamycin sensitivity under aerobic condition. Upon submergence, yeast and human FKBP12 can significantly block cotyledon greening while Arabidopsis FKBP12 only retards plant growth in the presence of rapamycin, suggesting that hypoxia stress could partially restore the functions of AtFKBP12 to bridge the interaction between rapamycin and TOR. To further determine if communication between TOR and auxin signaling exists in plants, yeast FKBP12 was introduced into DR5::GUS homozygous plants. The transgenic plants DR5/BP12 were then treated with rapamycin or KU63794 (a new inhibitor of TOR). GUS staining showed that the auxin content of root tips decreased compared to the control. DR5/BP12 plants lost sensitivity to auxin after treatment with rapamycin. Auxin-defective phenotypes, including short primary roots, fewer lateral roots, and loss of gravitropism, occurred in DR5/BP12 plants when seedlings were treated with rapamycin+KU63794. This indicated that the combination of rapamycin and KU63794 can significantly inhibit TOR and auxin signaling in DR5/BP12 plants. These studies demonstrate that TOR is essential for auxin signaling transduction in Arabidopsis.
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Affiliation(s)
- Kexuan Deng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Xianzhe Zheng
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Kang Zhang
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Wanjing Wang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Pan Dong
- School of Life Sciences, Chongqing UniversityChongqing, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing UniversityChongqing, China
- *Correspondence: Maozhi Ren
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21
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Dobrenel T, Mancera-Martínez E, Forzani C, Azzopardi M, Davanture M, Moreau M, Schepetilnikov M, Chicher J, Langella O, Zivy M, Robaglia C, Ryabova LA, Hanson J, Meyer C. The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6. FRONTIERS IN PLANT SCIENCE 2016; 7:1611. [PMID: 27877176 PMCID: PMC5100631 DOI: 10.3389/fpls.2016.01611] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/12/2016] [Indexed: 05/05/2023]
Abstract
Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.
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Affiliation(s)
- Thomas Dobrenel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- Université Paris-Sud–Université Paris-SaclayOrsay, France
- Umeå Plant Science Center, Department of Plant Physiology, Umeå UniversityUmeå, Sweden
| | - Eder Mancera-Martínez
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Céline Forzani
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
| | - Marianne Azzopardi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
| | | | - Manon Moreau
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix-Marseille Université, Faculté des Sciences de LuminyMarseille, France
| | - Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Johana Chicher
- Plateforme Protéomique Strasbourg-Esplanade, CNRS FRC1589, Institut de Biologie Moléculaire et CellulaireStrasbourg, France
| | | | - Michel Zivy
- Plateforme PAPPSO, UMR GQE-Le MoulonGif sur Yvette, France
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix-Marseille Université, Faculté des Sciences de LuminyMarseille, France
| | - Lyubov A. Ryabova
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå UniversityUmeå, Sweden
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- *Correspondence: Christian Meyer,
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22
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Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE. Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways. Mol Cell Proteomics 2015; 14:2243-60. [PMID: 26091701 DOI: 10.1074/mcp.m114.047183] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Indexed: 01/01/2023] Open
Abstract
The circadian clock provides adaptive advantages to an organism, resulting in increased fitness and survival. The phosphorylation events that regulate circadian-dependent signaling and the processes which post-translationally respond to clock-gated signals are largely unknown. To better elucidate post-translational events tied to the circadian system we carried out a survey of circadian-regulated protein phosphorylation events in Arabidopsis seedlings. A large-scale mass spectrometry-based quantitative phosphoproteomics approach employing TiO2-based phosphopeptide enrichment techniques identified and quantified 1586 phosphopeptides on 1080 protein groups. A total of 102 phosphopeptides displayed significant changes in abundance, enabling the identification of specific patterns of response to circadian rhythms. Our approach was sensitive enough to quantitate oscillations in the phosphorylation of low abundance clock proteins (early flowering4; ELF4 and pseudoresponse regulator3; PRR3) as well as other transcription factors and kinases. During constant light, extensive cyclic changes in phosphorylation status occurred in critical regulators, implicating direct or indirect regulation by the circadian system. These included proteins influencing transcriptional regulation, translation, metabolism, stress and phytohormones-mediated responses. We validated our analysis using the elf4-211 allele, in which an S45L transition removes the phosphorylation herein identified. We show that removal of this phosphorylatable site diminishes interaction with early flowering3 (ELF3), a key partner in a tripartite evening complex required for circadian cycling. elf4-211 lengthens period, which increases with increasing temperature, relative to the wild type, resulting in a more stable temperature compensation of circadian period over a wider temperature range.
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Affiliation(s)
- Mani Kant Choudhary
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea
| | - Yuko Nomura
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Lei Wang
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210; ‖Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hirofumi Nakagami
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - David E Somers
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
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23
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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24
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Roy B, von Arnim AG. Translational Regulation of Cytoplasmic mRNAs. THE ARABIDOPSIS BOOK 2013; 11:e0165. [PMID: 23908601 PMCID: PMC3727577 DOI: 10.1199/tab.0165] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation. We begin by introducing essential features of the translation apparatus. We summarize early evidence for translational control from the pre-Arabidopsis era. Next, we review evidence for translation control in response to stress, to metabolites, and in development. The following section emphasizes RNA sequence elements and biochemical processes that regulate translation. We close with a chapter on the role of signaling pathways that impinge on translation.
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Affiliation(s)
- Bijoyita Roy
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Current address: University of Massachussetts Medical School, Worcester, MA 01655-0122, USA
| | - Albrecht G. von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
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25
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Schepetilnikov M, Dimitrova M, Mancera-Martínez E, Geldreich A, Keller M, Ryabova LA. TOR and S6K1 promote translation reinitiation of uORF-containing mRNAs via phosphorylation of eIF3h. EMBO J 2013; 32:1087-102. [PMID: 23524850 DOI: 10.1038/emboj.2013.61] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 02/15/2013] [Indexed: 11/09/2022] Open
Abstract
Mammalian target-of-rapamycin (mTOR) triggers S6 kinase (S6K) activation to phosphorylate targets linked to translation in response to energy, nutrients, and hormones. Pathways of TOR activation in plants remain unknown. Here, we uncover the role of the phytohormone auxin in TOR signalling activation and reinitiation after upstream open reading frame (uORF) translation, which in plants is dependent on translation initiation factor eIF3h. We show that auxin triggers TOR activation followed by S6K1 phosphorylation at T449 and efficient loading of uORF-mRNAs onto polysomes in a manner sensitive to the TOR inhibitor Torin-1. Torin-1 mediates recruitment of inactive S6K1 to polysomes, while auxin triggers S6K1 dissociation and recruitment of activated TOR instead. A putative target of TOR/S6K1-eIF3h-is phosphorylated and detected in polysomes in response to auxin. In TOR-deficient plants, polysomes were prebound by inactive S6K1, and loading of uORF-mRNAs and eIF3h was impaired. Transient expression of eIF3h-S178D in plant protoplasts specifically upregulates uORF-mRNA translation. We propose that TOR functions in polysomes to maintain the active S6K1 (and thus eIF3h) phosphorylation status that is critical for translation reinitiation.
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Affiliation(s)
- Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg Cedex 67084, France
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26
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Ortega JL, Wilson OL, Sengupta-Gopalan C. The 5' untranslated region of the soybean cytosolic glutamine synthetase β(1) gene contains prokaryotic translation initiation signals and acts as a translational enhancer in plants. Mol Genet Genomics 2012; 287:881-93. [PMID: 23080263 PMCID: PMC3881598 DOI: 10.1007/s00438-012-0724-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 10/04/2012] [Indexed: 01/03/2023]
Abstract
Glutamine synthetase (GS) catalyzes the synthesis of glutamine from glutamate and ammonia. In plants, it occurs as two major isoforms, a cytosolic form (GS(1)) and a nuclear encoded chloroplastic form. The focus of this paper is to determine the role of the 5'UTR of a GS(1) gene. GS(1) gene constructs with and without its 5' and 3' UTRs, driven by a constitutive promoter, were agroinfiltrated into tobacco leaves and the tissues were analyzed for both transgene transcript and protein accumulation. The constructs were also tested in an in vitro transcription/translation system and in Escherichia coli. Our results showed that while the 3'UTR functioned in the destabilization of the transcript, the 5'UTR acted as a translation enhancer in plant cells but not in the in vitro translation system. The 5'UTR of the GS(1) gene when placed in front of a reporter gene (uidA), showed a 20-fold increase in the level of GUS expression in agroinfiltrated leaves when compared to the same gene construct without the 5'UTR. The 5'UTR-mediated translational enhancement is probably another step in the regulation of GS in plants. The presence of the GS(1) 5'UTR in front of the GS(1) coding region allowed for its translation in E. coli suggesting the commonality of the translation initiation mechanism for this gene between plants and bacteria.
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Affiliation(s)
- Jose Luis Ortega
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Olivia L. Wilson
- Molecular Biology Graduate Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Champa Sengupta-Gopalan
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA,
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27
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Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors. Proc Natl Acad Sci U S A 2012; 109:19537-44. [PMID: 23144218 DOI: 10.1073/pnas.1214774109] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Upstream ORFs are elements found in the 5'-leader sequences of specific mRNAs that modulate the translation of downstream ORFs encoding major gene products. In Arabidopsis, the translational control of auxin response factors (ARFs) by upstream ORFs has been proposed as a regulatory mechanism required to respond properly to complex auxin-signaling inputs. In this study, we identify and characterize the aberrant auxin responses in specific ribosomal protein mutants in which multiple ARF transcription factors are simultaneously repressed at the translational level. This characteristic lends itself to the use of these mutants as genetic tools to bypass the genetic redundancy among members of the ARF family in Arabidopsis. Using this approach, we were able to assign unique functions for ARF2, ARF3, and ARF6 in plant development.
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28
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Turkina MV, Klang Årstrand H, Vener AV. Differential phosphorylation of ribosomal proteins in Arabidopsis thaliana plants during day and night. PLoS One 2011; 6:e29307. [PMID: 22195043 PMCID: PMC3241707 DOI: 10.1371/journal.pone.0029307] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/24/2011] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis in plants is characterized by increase in the translation rates for numerous proteins and central metabolic enzymes during the day phase of the photoperiod. The detailed molecular mechanisms of this diurnal regulation are unknown, while eukaryotic protein translation is mainly controlled at the level of ribosomal initiation complexes, which also involves multiple events of protein phosphorylation. We characterized the extent of protein phosphorylation in cytosolic ribosomes isolated from leaves of the model plant Arabidopsis thaliana harvested during day or night. Proteomic analyses of preparations corresponding to both phases of the photoperiod detected phosphorylation at eight serine residues in the C-termini of six ribosomal proteins: S2-3, S6-1, S6-2, P0-2, P1 and L29-1. This included previously unknown phosphorylation of the 40S ribosomal protein S6 at Ser-231. Relative quantification of the phosphorylated peptides using stable isotope labeling and mass spectrometry revealed a 2.2 times increase in the day/night phosphorylation ratio at this site. Phosphorylation of the S6-1 and S6-2 variants of the same protein at Ser-240 increased by the factors of 4.2 and 1.8, respectively. The 1.6 increase in phosphorylation during the day was also found at Ser-58 of the 60S ribosomal protein L29-1. It is suggested that differential phosphorylation of the ribosomal proteins S6-1, S6-2 and L29-1 may contribute to modulation of the diurnal protein synthesis in plants.
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Affiliation(s)
- Maria V. Turkina
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Hanna Klang Årstrand
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Alexander V. Vener
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- * E-mail:
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29
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Ferro N, Bredow T, Jacobsen HJ, Reinard T. Route to Novel Auxin: Auxin Chemical Space toward Biological Correlation Carriers. Chem Rev 2010; 110:4690-708. [DOI: 10.1021/cr800229s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noel Ferro
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, Bonn, Germany 53115 and Institute for Plant Genetics, Leibniz University of Hannover, Germany
| | - Thomas Bredow
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, Bonn, Germany 53115 and Institute for Plant Genetics, Leibniz University of Hannover, Germany
| | - Hans-Jorg Jacobsen
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, Bonn, Germany 53115 and Institute for Plant Genetics, Leibniz University of Hannover, Germany
| | - Thomas Reinard
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, Bonn, Germany 53115 and Institute for Plant Genetics, Leibniz University of Hannover, Germany
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30
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Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol 2006; 7:847-59. [PMID: 16990790 DOI: 10.1038/nrm2020] [Citation(s) in RCA: 673] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hormones have been at the centre of plant physiology research for more than a century. Research into plant hormones (phytohormones) has at times been considered as a rather vague subject, but the systematic application of genetic and molecular techniques has led to key insights that have revitalized the field. In this review, we will focus on the plant hormone auxin and its action. We will highlight recent mutagenesis and molecular studies, which have delineated the pathways of auxin transport, perception and signal transduction, and which together define the roles of auxin in controlling growth and patterning.
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Affiliation(s)
- William D Teale
- Institut für Biologie II/Botanik, Schänzlestrasse 1, 79104 Freiburg, Germany
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31
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McIntosh KB, Bonham-Smith PC. Ribosomal protein gene regulation: what about plants? ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribosome is an intricate ribonucleoprotein complex with a multitude of protein constituents present in equimolar amounts. Coordination of the synthesis of these ribosomal proteins (r-proteins) presents a major challenge to the cell. Although most r-proteins are highly conserved, the mechanisms by which r-protein gene expression is regulated often differ widely among species. While the primary regulatory mechanisms coordinating r-protein synthesis in bacteria, yeast, and animals have been identified, the mechanisms governing the coordination of plant r-protein expression remain largely unexplored. In addition, plants are unique among eukaryotes in carrying multiple (often more than two) functional genes encoding each r-protein, which substantially complicates coordinate expression. A survey of the current knowledge regarding coordinated systems of r-protein gene expression in different model organisms suggests that vertebrate r-protein gene regulation provides a valuable comparison for plants.
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Affiliation(s)
- Kerri B. McIntosh
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Peta C. Bonham-Smith
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
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32
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Wang H, Zheng HQ, Sha W, Zeng R, Xia QC. A proteomic approach to analysing responses of Arabidopsis thaliana callus cells to clinostat rotation. JOURNAL OF EXPERIMENTAL BOTANY 2006; 57:827-35. [PMID: 16449375 DOI: 10.1093/jxb/erj066] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Callus cells of Arabidopsis thaliana (cv. Landsberg erecta) were exposed for 8 h to a horizontal clinostat rotation (H, simulated weightlessness), a vertical clinostat rotation (V, clinostat control), or a stationary control (S) growth condition. The amount of glucose and fructose apparently decreased, while starch content increased in the H compared with the V- and S-treated cells. In order to investigate the influences of clinostat rotation on the cellular proteome further, the proteome alterations induced by horizontal and vertical clinostat rotation have been comparatively analysed by high-resolution two-dimensional (2-D) gel electrophoresis and mass spectrometry. Image analysis of silver-stained 2-D gels revealed that 80 protein spots showed quantitative and qualitative variations that were significantly (P <0.01) and reproducibly different between the clinorotated (H or V) and the stationary control samples. Protein spots excised from 2-D gels were analysed by microbe high performance liquid chromatography-ion trap-mass spectrometry (LC-IT-MS) to obtain the tandem mass (MS/MS) spectra. 18 protein spots, which showed significant expression alteration only under the H condition compared with those under V and S conditions, were identified. Of these proteins, seven were involved in stress responses, and four protein spots were identified as key enzymes in carbohydrate metabolism and lipid biosynthesis. Two reversibly glycosylated cell wall proteins were down-regulated in the H samples. Other proteins such as protein disulphide isomerase, transcription initiation factor IIF, and two ribosomal proteins also exhibited altered expression under the H condition. The data presented in this study illustrate that clinostat rotation of Arabidopsis callus cells has a significant impact on the expression of proteins involved in general stress responses, metabolic pathways, gene activation/transcription, protein synthesis, and cell wall biosynthesis.
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Affiliation(s)
- Hui Wang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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33
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Casati P, Walbot V. Crosslinking of ribosomal proteins to RNA in maize ribosomes by UV-B and its effects on translation. PLANT PHYSIOLOGY 2004; 136:3319-32. [PMID: 15466230 PMCID: PMC523391 DOI: 10.1104/pp.104.047043] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Ultraviolet-B (UV-B) photons can cause substantial cellular damage in biomolecules, as is well established for DNA. Because RNA has the same absorption spectrum for UV as DNA, we have investigated damage to this cellular constituent. In maize (Zea mays) leaves, UV-B radiation damages ribosomes by crosslinking cytosolic ribosomal proteins S14, L23a, and L32, and chloroplast ribosomal protein L29 to RNA. Ribosomal damage accumulated during a day of UV-B exposure correlated with a progressive decrease in new protein production; however, de novo synthesis of some ribosomal proteins is increased after 6 h of UV-B exposure. After 16 h without UV-B, damaged ribosomes were eliminated and translation was restored to normal levels. Ribosomal protein S6 and an S6 kinase are phosphorylated during UV-B exposure; these modifications are associated with selective translation of some ribosomal proteins after ribosome damage in mammalian fibroblast cells and may be an adaptation in maize. Neither photosynthesis nor pigment levels were affected significantly by UV-B, demonstrating that the treatment applied is not lethal and that maize leaf physiology readily recovers.
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Affiliation(s)
- Paula Casati
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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34
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Rhoads DM, Vanlerberghe GC. Mitochondria-Nucleus Interactions: Evidence for Mitochondrial Retrograde Communication in Plant Cells. PLANT MITOCHONDRIA: FROM GENOME TO FUNCTION 2004. [DOI: 10.1007/978-1-4020-2400-9_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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35
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Williams AJ, Werner-Fraczek J, Chang IF, Bailey-Serres J. Regulated phosphorylation of 40S ribosomal protein S6 in root tips of maize. PLANT PHYSIOLOGY 2003; 132:2086-97. [PMID: 12913163 PMCID: PMC181292 DOI: 10.1104/pp.103.022749] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Revised: 03/27/2003] [Accepted: 04/02/2003] [Indexed: 05/18/2023]
Abstract
Ribosomal protein S6 (RPS6) is located in the mRNA binding site of the 40S subunit of cytosolic ribosomes. Two maize (Zea mays) rps6 genes were identified that encode polypeptides (30 kD, 11.4 pI) with strong primary amino acid sequence and predicted secondary structure similarity to RPS6 of other eukaryotes. Maize RPS6 was analyzed by the use of two-dimensional gel electrophoresis systems, in vivo labeling with [(32)P]P(i) and immunological detection. Nine RPS6 isoforms were resolved in a two-dimensional basic-urea/sodium dodecyl sulfate-polyacrylamide gel electrophoresis system. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry performed on trypsin-digested isoforms identified four serine (Ser) and one threonine (Thr) residue in the carboxy-terminal region as phosphorylation sites (RRS(238)KLS(241)AAAKAS(247)AAT(250)S(251)A-COOH). Heterogeneity in RPS6 phosphorylation was a consequence of the presence of zero to five phosphorylated residues. Phosphorylated isoforms fell into two groups characterized by (a) sequential phosphorylation of Ser-238 and Ser-241 and (b) the absence of phospho-Ser-238 and presence of phospho-Ser-241. The accumulation of hyper-phosphorylated isoforms with phospho-Ser-238 was reduced in response to oxygen deprivation and heat shock, whereas accumulation of these isoforms was elevated by cold stress. Salt and osmotic stress had no reproducible effect on RPS6 phosphorylation. The reduction in hyper-phosphorylated isoforms under oxygen deprivation was blocked by okadaic acid, a Ser/Thr phosphatase inhibitor. By contrast, the recovery of hyper-phosphorylated isoforms upon re-oxygenation was blocked by LY-294002, an inhibitor of phosphatidylinositol 3-kinases. Thus, differential activity of phosphatase(s) and kinase(s) determine complex heterogeneity in RPS6 phosphorylation.
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Affiliation(s)
- Alan J Williams
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124, USA
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