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Blázquez MA. Polyamines: Their Role in Plant Development and Stress. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:95-117. [PMID: 38382905 DOI: 10.1146/annurev-arplant-070623-110056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
This review focuses on the intricate relationship between plant polyamines and the genetic circuits and signaling pathways that regulate various developmental programs and the defense responses of plants when faced with biotic and abiotic aggressions. Particular emphasis is placed on genetic evidence supporting the involvement of polyamines in specific processes, such as the pivotal role of thermospermine in regulating xylem cell differentiation and the significant contribution of polyamine metabolism in enhancing plant resilience to drought. Based on the numerous studies describing effects of the manipulation of plant polyamine levels, two conceptually different mechanisms for polyamine activity are discussed: direct participation of polyamines in translational regulation and the indirect production of hydrogen peroxide as a defensive mechanism against pathogens. By describing the multifaceted functions of polyamines, this review underscores the profound significance of these compounds in enabling plants to adapt and thrive in challenging environments.
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Affiliation(s)
- Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain;
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2
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D'Incà R, Mattioli R, Tomasella M, Tavazza R, Macone A, Incocciati A, Martignago D, Polticelli F, Fraudentali I, Cona A, Angelini R, Tavazza M, Nardini A, Tavladoraki P. A Solanum lycopersicum polyamine oxidase contributes to the control of plant growth, xylem differentiation, and drought stress tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:960-981. [PMID: 38761363 DOI: 10.1111/tpj.16809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/26/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024]
Abstract
Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD-dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back-conversion of thermospermine (T-Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T-Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9-mediated loss-of-function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T-Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin- and gibberellin-related genes compared to wild-type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T-Spm-mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T-Spm role in improving stress tolerance while not constraining growth.
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Affiliation(s)
- Riccardo D'Incà
- Department of Science, University Roma Tre, 00146, Rome, Italy
| | | | - Martina Tomasella
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Raffaela Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), BIOAG-BIOTEC C.R. Casaccia, Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, Rome, Italy
| | - Alessio Incocciati
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, Rome, Italy
| | | | - Fabio Polticelli
- Department of Science, University Roma Tre, 00146, Rome, Italy
- National Institute of Nuclear Physics, Roma Tre Section, 00146, Rome, Italy
| | | | - Alessandra Cona
- Department of Science, University Roma Tre, 00146, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Riccardo Angelini
- Department of Science, University Roma Tre, 00146, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi (INBB), Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Mario Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), BIOAG-BIOTEC C.R. Casaccia, Rome, Italy
| | - Andrea Nardini
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Paraskevi Tavladoraki
- Department of Science, University Roma Tre, 00146, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi (INBB), Rome, Italy
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Takahashi Y. ACL5 acquired strict thermospermine synthesis activity during the emergence of vascular plants. THE NEW PHYTOLOGIST 2024; 242:2669-2681. [PMID: 38587066 DOI: 10.1111/nph.19733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024]
Abstract
Norspermine (Nspm), one of the uncommon polyamines (PAs), was detected in bryophytes and lycophytes; therefore, the aminopropyltransferases involved in the synthesis of Nspm were investigated. The enzymatic activity was evaluated by the transient high expression of various aminopropyltransferase genes in Nicotiana benthamiana, followed by quantification of PA distribution in the leaves using gas chromatography-mass spectrometry. The bryophyte orthologues of ACL5, which is known to synthesise thermospermine (Tspm) in flowering plants, were found to have strong Nspm synthesis activity. In addition, two ACL5 orthologous with different substrate specificities were conserved in Selaginella moellendorffii, one of which was involved in Tspm synthesis and the other in Nspm synthesis. Therefore, further detailed analysis using these two factors revealed that the β-hairpin structural region consisting of β-strands 1 and 2 at the N-terminus of ACL5 is involved in substrate specificity. Through functional analysis of a total of 40 ACL5 genes in 33 organisms, including algae, it was shown that ACL5 has changed its substrate specificity several times during plant evolution and diversification. Furthermore, it was strongly suggested that ACL5 acquired strict Tspm synthesis activity during the emergence of vascular plants, especially through major changes around the β-hairpin structural region.
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Affiliation(s)
- Yoshihiro Takahashi
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
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4
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Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Furumoto T, Yamaoka S, Kohchi T, Motose H, Takahashi T. Thermospermine Is an Evolutionarily Ancestral Phytohormone Required for Organ Development and Stress Responses in Marchantia Polymorpha. PLANT & CELL PHYSIOLOGY 2024; 65:460-471. [PMID: 38179828 PMCID: PMC11020214 DOI: 10.1093/pcp/pcae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
Thermospermine suppresses auxin-inducible xylem differentiation, whereas its structural isomer, spermine, is involved in stress responses in angiosperms. The thermospermine synthase, ACAULIS5 (ACL5), is conserved from algae to land plants, but its physiological functions remain elusive in non-vascular plants. Here, we focused on MpACL5, a gene in the liverwort Marchantia polymorpha, that rescued the dwarf phenotype of the acl5 mutant in Arabidopsis. In the Mpacl5 mutants generated by genome editing, severe growth retardation was observed in the vegetative organ, thallus, and the sexual reproductive organ, gametangiophore. The mutant gametangiophores exhibited remarkable morphological defects such as short stalks, fasciation and indeterminate growth. Two gametangiophores fused together, and new gametangiophores were often initiated from the old ones. Furthermore, Mpacl5 showed altered responses to heat and salt stresses. Given the absence of spermine in bryophytes, these results suggest that thermospermine has a dual primordial function in organ development and stress responses in M. polymorpha. The stress response function may have eventually been assigned to spermine during land plant evolution.
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Affiliation(s)
- Takuya Furumoto
- Department of Biological Science, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Hiroyasu Motose
- Department of Biological Science, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530 Japan
| | - Taku Takahashi
- Department of Biological Science, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530 Japan
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Mai H, Qin T, Wei H, Yu Z, Pang G, Liang Z, Ni J, Yang H, Tang H, Xiao L, Liu H, Liu T. Overexpression of OsACL5 triggers environmentally-dependent leaf rolling and reduces grain size in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:833-847. [PMID: 37965680 PMCID: PMC10955489 DOI: 10.1111/pbi.14227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/21/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
Major polyamines include putrescine, spermidine, spermine and thermospermine, which play vital roles in growth and adaptation against environmental changes in plants. Thermospermine (T-Spm) is synthetised by ACL5. The function of ACL5 in rice is still unknown. In this study, we used a reverse genetic strategy to investigate the biological function of OsACL5. We generated several knockout mutants by pYLCRISPR/Cas9 system and overexpressing (OE) lines of OsACL5. Interestingly, the OE plants exhibited environmentally-dependent leaf rolling, smaller grains, lighter 1000-grain weight and reduction in yield per plot. The area of metaxylem vessels of roots and leaves of OE plants were significantly smaller than those of WT, which possibly caused reduction in leaf water potential, resulting in leaf rolling with rise in the environmental temperature and light intensity and decrease in humidity. Additionally, the T-Spm contents were markedly increased by over ninefold whereas the ethylene evolution was reduced in OE plants, suggesting that T-Spm signalling pathway interacts with ethylene pathway to regulate multiple agronomic characters. Moreover, the osacl5 exhibited an increase in grain length, 1000-grain weight, and yield per plot. OsACL5 may affect grain size via mediating the expression of OsDEP1, OsGS3 and OsGW2. Furthermore, haplotypes analysis indicated that OsACL5 plays a conserved function on regulating T-Spm levels during the domestication of rice. Our data demonstrated that identification of OsACL5 provides a theoretical basis for understanding the physiological mechanism of T-Spm which may play roles in triggering environmentally dependent leaf rolling; OsACL5 will be an important gene resource for molecular breeding for higher yield.
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Affiliation(s)
- Huafu Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Tian Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Huan Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Zhen Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Gang Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Zhiman Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Jiansheng Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Haishan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Haiying Tang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Lisi Xiao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Huili Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Taibo Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
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7
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Solé-Gil A, Úrbez C, Ferrando A, Blázquez MA. Quantification of Xylem-Specific Thermospermine-Dependent Translation of SACL Transcripts with Dual Luciferase Reporter System. Methods Mol Biol 2024; 2722:79-87. [PMID: 37897601 DOI: 10.1007/978-1-0716-3477-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
Thermospermine (Tspm) is a polyamine found to play a crucial role in xylem development in Arabidopsis thaliana. Tspm promotes the translation of the SACL genes by counteracting the activity of a cis element in their 5'-leader region that suppresses the translation of the main ORF. Here we describe a method to test the Tspm-dependent translational regulation of the 5'-leader of the SACL mRNAs in Nicotiana benthamiana leaves and A. thaliana mesophyll protoplasts with a dual luciferase assay. The dual luciferase reporter system is used to assess gene expression and is based on the detection of the Firefly luciferase luminescence driven by a specific promoter. However, it can also be used to evaluate the cis elements found in 5'-leader that influence the translation of the main ORF in a transcript. We have used a modified version of the pGreenII 0800 LUC plasmid carrying a double 35S promoter, followed by a poly-linker sequence in phase with the Firefly luciferase gene (pGreen2x35SLUC) where the full 5'-leader sequence of SACL3 was cloned. This construct was used for Agrobacterium tumefaciens infiltration of N. benthamiana leaves and for transfection of A. thaliana mesophyll protoplasts, followed by mock or Tspm treatments. The resulting translation of the Firefly luciferase in these organisms and conditions was then tested by measuring luminescence with the dual luciferase assay and a luminometer. These experiments have allowed us to quantify the positive effect of Tspm in the translation of SACL3 transcripts.
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Affiliation(s)
- Anna Solé-Gil
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), Valencia, Spain
| | - Cristina Úrbez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), Valencia, Spain
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), Valencia, Spain.
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Nishii Y, Koyama D, Fukushima H, Takahashi T. Suppression of the dwarf phenotype of an Arabidopsis mutant defective in thermospermine biosynthesis by a synonymous codon change in the SAC51 uORF. Mol Genet Genomics 2023; 298:1505-1514. [PMID: 37845372 DOI: 10.1007/s00438-023-02076-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/01/2023] [Indexed: 10/18/2023]
Abstract
Thermospermine plays a critical role in negatively regulating xylem development in angiosperms. A mutant of Arabidopsis thaliana that is defective in thermospermine biosynthesis, acaulis5 (acl5), exhibits a dwarf phenotype with excessive xylem formation. Mechanistically thermospermine acts in attenuating the inhibitory effect of an evolutionarily conserved upstream open reading frame (uORF) on the main ORF of SAC51, which encodes a basic helix-loop-helix protein involved in xylem repression. Here, we revealed that a semidominant suppressor of acl5, sac503, which partially restores the acl5 phenotype, has a point mutation in the conserved uORF of SAC51 with no amino acid substitution in the deduced peptide sequence. In transgenic lines carrying the β-glucuronidase (GUS) reporter gene fused with the SAC51 5' region containing the uORF, the mutant construct was shown to confer higher GUS activity than does the wild-type SAC51 construct. We confirmed that sac503 mRNA was more stable than SAC51 mRNA in acl5. These results suggest that the single-base change in sac503 positively affects the translation of its main ORF instead of thermospermine. We further found that the uORF-GUS fusion protein could be synthesized in planta from the wild-type and sac503 translational fusion constructs.
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Affiliation(s)
- Yuichi Nishii
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700 8530, Japan
| | - Daiki Koyama
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700 8530, Japan
| | - Hiroko Fukushima
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700 8530, Japan
| | - Taku Takahashi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700 8530, Japan.
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9
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Matsuo H, Fukushima H, Kurokawa S, Kawano E, Okamoto T, Motose H, Takahashi T. Loss of function of an Arabidopsis homologue of JMJD6 suppresses the dwarf phenotype of acl5, a mutant defective in thermospermine biosynthesis. FEBS Lett 2022; 596:3005-3014. [PMID: 35962471 DOI: 10.1002/1873-3468.14470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022]
Abstract
In Arabidopsis thaliana, the ACL5 gene encodes thermospermine synthase and its mutant, acl5, exhibits a dwarf phenotype with excessive xylem formation. Studies of suppressor mutants of acl5 reveal the involvement of thermospermine in enhancing mRNA translation of the SAC51 gene family. We show here that a mutant, sac59, which partially suppresses the acl5 phenotype, has a point mutation in JMJ22 encoding a D6-class Jumonji C protein (JMJD6). A T-DNA insertion allele, jmj22-2, also partially suppressed the acl5 phenotype while mutants of its closest two homologs JMJ21 and JMJ20 had no such effects, suggesting a unique role for JMJ22 in plant development. We found that mRNAs of the SAC51 family are more stabilized in acl5 jmj22-2 than in acl5.
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Affiliation(s)
- Hirotoshi Matsuo
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hiroko Fukushima
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shinpei Kurokawa
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Eri Kawano
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Takashi Okamoto
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hiroyasu Motose
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Taku Takahashi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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10
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Causier B, Hopes T, McKay M, Paling Z, Davies B. Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation. PLANT, CELL & ENVIRONMENT 2022; 45:1229-1241. [PMID: 35128674 PMCID: PMC9305500 DOI: 10.1111/pce.14277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 05/08/2023]
Abstract
The regulation of protein synthesis plays an important role in the growth and development of all organisms. Upstream open reading frames (uORFs) are commonly found in eukaryotic messenger RNA transcripts and typically attenuate the translation of associated downstream main ORFs (mORFs). Conserved peptide uORFs (CPuORFs) are a rare subset of uORFs, some of which have been shown to conditionally regulate translation by ribosome stalling. Here, we show that Arabidopsis CPuORF19, CPuORF46 and CPuORF47, which are ancient in origin, regulate translation of any downstream ORF, in response to the agriculturally significant environmental signals, heat stress and water limitation. Consequently, these CPuORFs represent a versatile toolkit for inducible gene expression with broad applications. Finally, we note that different classes of CPuORFs may operate during distinct phases of translation, which has implications for the bioengineering of these regulatory factors.
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Affiliation(s)
- Barry Causier
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Mary McKay
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Zachary Paling
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Brendan Davies
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
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11
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Afonnikov DA, Sinitsyna OI, Golubeva TS, Shmakov NA, Kochetov AV. [Ribosomal profiling as a tool for studying translation in plants: main results, problems and future prospects]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:251-259. [PMID: 34901721 PMCID: PMC8627869 DOI: 10.18699/vj21.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 11/19/2022] Open
Abstract
The expression of eukaryotic genes can be regulated at several stages, including the translation of mRNA. It is known that the structure of mRNA can affect both the efficiency of interaction with the translation apparatus in general and the choice of translation initiation sites. To study the translated fraction of the transcriptome, experimental methods of analysis were developed, the most informative of which is ribosomal profiling (RP, Ribo-seq). Originally developed for use in yeast systems, this method has been adapted for research in translation mechanisms in many plant species. This technology includes the isolation of the polysomal fraction and high-performance sequencing of a pool of mRNA fragments associated with ribosomes. Comparing the results of transcript coverage with reads obtained using the ribosome profiling with the transcriptional efficiency of genes allows the translation efficiency to be evaluated for each transcript. The exact positions of ribosomes determined on mRNA sequences allow determining the translation of open reading frames and switching between the translation of several reading frames - a phenomenon in which two or more overlapping frames are read from one mRNA and different proteins are synthesized. The advantage of this method is that it provides quantitative estimates of ribosome coverage of mRNA and can detect relatively rare translation events. Using this technology, it was possible to identify and classify plant genes by the type of regulation of their expression at the transcription, translation, or both levels. Features of the mRNA structure that affect translation levels have been revealed: the formation of G2 quadruplexes and the presence of specific motifs in the 5'-UTR region, GC content, the presence of alternative translation starts, and the influence of uORFs on the translation of downstream mORFs. In this review, we briefly reviewed the RP methodology and the prospects for its application to study the structural and functional organization and regulation of plant gene expression.
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Affiliation(s)
- D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - O I Sinitsyna
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - T S Golubeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - N A Shmakov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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12
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Translational and post-translational regulation of polyamine metabolic enzymes in plants. J Biotechnol 2021; 344:1-10. [PMID: 34915092 DOI: 10.1016/j.jbiotec.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/19/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
Polyamines are small organic and basic polycations that perform essential regulatory functions in all living organisms. Fluctuations in polyamine content have been observed to occur during growth, development and under stress conditions, implying that polyamines play pivotal roles in diverse cellular and physiological processes. To achieve polyamine homeostasis, the entire metabolic pathway is subjected to a fine-tuned regulation of its biosynthetic and catabolic genes and enzymes. In this review, we describe and discuss the most important mechanisms implicated in the translational and post-translational regulation of polyamine metabolic enzymes in plants. At the translational level, we emphasize the role of polyamines in the modulation of upstream open reading frame (uORF) activities that control the translation of polyamine biosynthetic and catabolic mRNAs. At the post-translational level, different aspects of the regulation of polyamine metabolic proteins are depicted, such as the proteolytic activation of enzyme precursors, the importance of dimerization in protein stability as well as in protein intracellular localization.
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13
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Milhinhos A, Bollhöner B, Blazquez MA, Novák O, Miguel CM, Tuominen H. ACAULIS5 Is Required for Cytokinin Accumulation and Function During Secondary Growth of Populus Trees. FRONTIERS IN PLANT SCIENCE 2020; 11:601858. [PMID: 33304375 PMCID: PMC7701098 DOI: 10.3389/fpls.2020.601858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
In the primary root and young hypocotyl of Arabidopsis, ACAULIS5 promotes translation of SUPPRESSOR OF ACAULIS51 (SAC51) and thereby inhibits cytokinin biosynthesis and vascular cell division. In this study, the relationships between ACAULIS5, SAC51 and cytokinin biosynthesis were investigated during secondary growth of Populus stems. Overexpression of ACAULIS5 from the constitutive 35S promoter in hybrid aspen (Populus tremula × Populus tremuloides) trees suppressed the expression level of ACAULIS5, which resulted in low levels of the physiologically active cytokinin bases as well as their direct riboside precursors in the transgenic lines. Low ACAULIS5 expression and low cytokinin levels of the transgenic trees coincided with low cambial activity of the stem. ACAULIS5 therefore, contrary to its function in young seedlings in Arabidopsis, stimulates cytokinin accumulation and cambial activity during secondary growth of the stem. This function is not derived from maturing secondary xylem tissues as transgenic suppression of ACAULIS5 levels in these tissues did not influence secondary growth. Interestingly, evidence was obtained for increased activity of the anticlinal division of the cambial initials under conditions of low ACAULIS5 expression and low cytokinin accumulation. We propose that ACAULIS5 integrates auxin and cytokinin signaling to promote extensive secondary growth of tree stems.
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Affiliation(s)
- Ana Milhinhos
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Benjamin Bollhöner
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Miguel A. Blazquez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia, Valencia, Spain
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany, Czech Academy of Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Célia M. Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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14
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Agustí J, Blázquez MA. Plant vascular development: mechanisms and environmental regulation. Cell Mol Life Sci 2020; 77:3711-3728. [PMID: 32193607 PMCID: PMC11105054 DOI: 10.1007/s00018-020-03496-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
Abstract
Plant vascular development is a complex process culminating in the generation of xylem and phloem, the plant transporting conduits. Xylem and phloem arise from specialized stem cells collectively termed (pro)cambium. Once developed, xylem transports mainly water and mineral nutrients and phloem transports photoassimilates and signaling molecules. In the past few years, major advances have been made to characterize the molecular, genetic and physiological aspects that govern vascular development. However, less is known about how the environment re-shapes the process, which molecular mechanisms link environmental inputs with developmental outputs, which gene regulatory networks facilitate the genetic adaptation of vascular development to environmental niches, or how the first vascular cells appeared as an evolutionary innovation. In this review, we (1) summarize the current knowledge of the mechanisms involved in vascular development, focusing on the model species Arabidopsis thaliana, (2) describe the anatomical effect of specific environmental factors on the process, (3) speculate about the main entry points through which the molecular mechanisms controlling of the process might be altered by specific environmental factors, and (4) discuss future research which could identify the genetic factors underlying phenotypic plasticity of vascular development.
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Affiliation(s)
- Javier Agustí
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022, Valencia, Spain.
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15
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Kage U, Powell JJ, Gardiner DM, Kazan K. Ribosome profiling in plants: what is not lost in translation? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5323-5332. [PMID: 32459844 DOI: 10.1093/jxb/eraa227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 05/03/2023]
Abstract
Translation is a highly dynamic cellular process whereby genetic information residing in an mRNA molecule is converted into a protein that in turn executes specific functions. However, pre-synthesized mRNA levels do not always correlate with corresponding protein levels, suggesting that translational control plays an essential role in gene regulation. A better understanding of how gene expression is regulated during translation will enable the discovery of new genes and mechanisms that control important traits in plants. Therefore, in recent years, several methods have been developed to analyse the translatome; that is, all mRNAs being actively translated at a given time, tissue, and/or developmental stage. Ribosome profiling or ribo-seq is one such technology revolutionizing our ability to analyse the translatome and in turn understand translational control of gene expression. Ribo-seq involves isolating mRNA-ribosome complexes, treating them with a RNase, and then identifying ribosome-protected mRNA regions by deep sequencing. Here, we briefly review recent ribosome profiling studies that revealed new insights into plant biology. Manipulation of novel genes identified using ribosome profiling could prove useful for increasing yield through improved biotic and abiotic stress tolerance.
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Affiliation(s)
- Udaykumar Kage
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Jonathan J Powell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
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16
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Dever TE, Ivanov IP, Sachs MS. Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation. Annu Rev Genet 2020; 54:237-264. [PMID: 32870728 DOI: 10.1146/annurev-genet-112618-043822] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA;
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17
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Liu J, Yang R, Jian N, Wei L, Ye L, Wang R, Gao H, Zheng Q. Putrescine metabolism modulates the biphasic effects of brassinosteroids on canola and Arabidopsis salt tolerance. PLANT, CELL & ENVIRONMENT 2020; 43:1348-1359. [PMID: 32176351 DOI: 10.1111/pce.13757] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 05/08/2023]
Abstract
Brassinosteroids (BRs) are known to improve salt tolerance of plants, but not in all situations. Here, we show that a certain concentration of 24-epibrassinolide (EBL), an active BR, can promote the tolerance of canola under high-salt stress, but the same concentration is disadvantageous under low-salt stress. We define this phenomenon as hormonal stress-level-dependent biphasic (SLDB) effects. The SLDB effects of EBL on salt tolerance in canola are closely related to H2 O2 accumulation, which is regulated by polyamine metabolism, especially putrescine (Put) oxidation. The inhibition of EBL on canola under low-salt stress can be ameliorated by repressing Put biosynthesis or diamine oxidase activity to reduce H2 O2 production. Genetic and phenotypic results of bri1-9, bak1, bes1-D, and bzr1-1D mutants and overexpression lines of BRI1 and BAK1 in Arabidopsis indicate that a proper enhancement of BR signaling benefits plants in countering salt stress, whereas excessive enhancement is just as harmful as a deficiency. These results highlight the involvement of crosstalk between BR signaling and Put metabolism in H2 O2 accumulation, which underlies the dual role of BR in plant salt tolerance.
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Affiliation(s)
- Jinlong Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ni Jian
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Long Wei
- College of Natural Resources and Environmental Science, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Liaoliao Ye
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ruihua Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Huiling Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Qingsong Zheng
- College of Natural Resources and Environmental Science, Nanjing Agricultural University, Nanjing, People's Republic of China
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18
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Takahashi H, Hayashi N, Hiragori Y, Sasaki S, Motomura T, Yamashita Y, Naito S, Takahashi A, Fuse K, Satou K, Endo T, Kojima S, Onouchi H. Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA. BMC Genomics 2020; 21:260. [PMID: 32228449 PMCID: PMC7106846 DOI: 10.1186/s12864-020-6662-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/10/2020] [Indexed: 12/27/2022] Open
Abstract
Background Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups. Results To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides. Conclusions This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan. .,Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan.
| | - Noriya Hayashi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yuta Hiragori
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shun Sasaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Taichiro Motomura
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Satoshi Naito
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Anna Takahashi
- Faculty of Information Technologies and Control, Belarusian State University of Informatics and Radio Electronics, 220013, Minsk, Belarus
| | - Kazuyuki Fuse
- New Business Development Office, Churitsu Electric Corporation, Toyoake, 470-1112, Japan
| | - Kenji Satou
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Toshinori Endo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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19
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Shinohara S, Okamoto T, Motose H, Takahashi T. Salt hypersensitivity is associated with excessive xylem development in a thermospermine-deficient mutant of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:374-383. [PMID: 31257654 DOI: 10.1111/tpj.14448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 05/21/2023]
Abstract
In Arabidopsis, spermine is produced in most tissues and has been implicated in stress response, while its structural isomer thermospermine is only in xylem precursor cells. Studies on acaulis5 (acl5), a mutant defective in the biosynthesis of thermospermine, have revealed that thermospermine plays a repressive role in xylem development through enhancement of mRNA translation of the SAC51 family. In contrast, the pao5 mutant defective in the degradation of thermospermine has high levels of thermospermine and shows increased salt tolerance, suggesting a role of thermospermine in salt stress response. Here we compared acl5 with a mutant of spermine synthase, spms, in terms of abiotic stress tolerance and found that acl5 was much more sensitive to sodium than the wild-type and spms. A double-mutant of acl5 and sac51-d, which suppresses the excessive xylem phenotype of acl5, recovered normal sensitivity, while a quadruple T-DNA insertion mutant of the SAC51 family, which has an increased thermospermine level but shows excessive xylem development, showed increased salt sensitivity, unlike pao5. Together with the result that the salt tolerance of both wild-type and acl5 seedlings was improved by long-term treatment with thermospermine, we suggest a correlation of the salt tolerance with reduced xylem development rather than with the thermospermine level. We further found that the mutants containing high thermospermine levels showed increased tolerance to drought and heat stress, suggesting another role of thermospermine that may be common with that of spermine and secondary to that in restricting excess xylem development associated with salt hypersensitivity.
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Affiliation(s)
- Shiori Shinohara
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, 700-8530, Okayama, Japan
| | - Takashi Okamoto
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, 700-8530, Okayama, Japan
| | - Hiroyasu Motose
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, 700-8530, Okayama, Japan
| | - Taku Takahashi
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, 700-8530, Okayama, Japan
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20
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Effect of Thermospermine on the Growth and Expression of Polyamine-Related Genes in Rice Seedlings. PLANTS 2019; 8:plants8080269. [PMID: 31390771 PMCID: PMC6724145 DOI: 10.3390/plants8080269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/27/2019] [Accepted: 08/05/2019] [Indexed: 12/28/2022]
Abstract
A mutant defective in the biosynthesis of thermospermine, acaulis5 (acl5), shows a dwarf phenotype with excess xylem vessels in Arabidopsis thaliana. Exogenous supply of thermospermine remarkably represses xylem differentiation in the root of seedlings, indicating the role of thermospermine in proper repression of xylem differentiation. However, the effect of thermospermine has rarely been investigated in other plant species. In this paper, we examined its effect on the growth and gene expression in rice seedlings. When grown with thermospermine, rice seedlings had no clearly enlarged metaxylem vessels in the root. Expression of OsACL5 was reduced in response to thermospermine, suggesting a negative feedback control of thermospermine biosynthesis like in Arabidopsis. Unlike Arabidopsis, however, rice showed up-regulation of phloem-expressed genes, OsHB5 and OsYSL16, by one-day treatment with thermospermine. Furthermore, expression of OsPAO2 and OsPAO6, encoding extracellular polyamine oxidase whose orthologs are not present in Arabidopsis, was induced by both thermospermine and spermine. These results suggest that thermospermine affects the expression of a subset of genes in rice different from those affected in Arabidopsis.
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21
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Solé-Gil A, Hernández-García J, López-Gresa MP, Blázquez MA, Agustí J. Conservation of Thermospermine Synthase Activity in Vascular and Non-vascular Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:663. [PMID: 31244864 PMCID: PMC6579911 DOI: 10.3389/fpls.2019.00663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/02/2019] [Indexed: 05/27/2023]
Abstract
In plants, the only confirmed function for thermospermine is regulating xylem cells maturation. However, genes putatively encoding thermospermine synthases have been identified in the genomes of both vascular and non-vascular plants. Here, we verify the activity of the thermospermine synthase genes and the presence of thermospermine in vascular and non-vascular land plants as well as in the aquatic plant Chlamydomonas reinhardtii. In addition, we provide information about differential content of thermospermine in diverse organs at different developmental stages in some vascular species that suggest that, although the major role of thermospermine in vascular plants is likely to be xylem development, other potential roles in development and/or responses to stress conditions could be associated to such polyamine. In summary, our results in vascular and non-vascular species indicate that the capacity to synthesize thermospermine is conserved throughout the entire plant kingdom.
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22
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Poidevin L, Unal D, Belda-Palazón B, Ferrando A. Polyamines as Quality Control Metabolites Operating at the Post-Transcriptional Level. PLANTS 2019; 8:plants8040109. [PMID: 31022874 PMCID: PMC6524035 DOI: 10.3390/plants8040109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/04/2023]
Abstract
Plant polyamines (PAs) have been assigned a large number of physiological functions with unknown molecular mechanisms in many cases. Among the most abundant and studied polyamines, two of them, namely spermidine (Spd) and thermospermine (Tspm), share some molecular functions related to quality control pathways for tightly regulated mRNAs at the level of translation. In this review, we focus on the roles of Tspm and Spd to facilitate the translation of mRNAs containing upstream ORFs (uORFs), premature stop codons, and ribosome stalling sequences that may block translation, thus preventing their degradation by quality control mechanisms such as the nonsense-mediated decay pathway and possible interactions with other mRNA quality surveillance pathways.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey.
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
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24
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Ishitsuka S, Yamamoto M, Miyamoto M, Kuwashiro Y, Imai A, Motose H, Takahashi T. Complexity and Conservation of Thermospermine-Responsive uORFs of SAC51 Family Genes in Angiosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:564. [PMID: 31118941 PMCID: PMC6504692 DOI: 10.3389/fpls.2019.00564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/15/2019] [Indexed: 05/10/2023]
Abstract
ACAULIS5 (ACL5) encodes thermospermine synthase in Arabidopsis and its loss-of-function mutant acl5 shows excess xylem differentiation and severe dwarfism. SAC51 encodes a basic helix-loop-helix (bHLH) protein and was identified from sac51-d, a dominant suppressor mutant of acl5, which restores the wild-type phenotype without thermospermine. The 5' leader of the SAC51 mRNA contains multiple upstream open-reading frames (uORFs) and sac51-d has a premature stop codon in the fourth uORF. This uORF is conserved among SAC51 family genes in vascular plants. According to the GUS reporter assay, the SAC51 promoter was not responsive to thermospermine but the SAC51 5' leader fused to the constitutive 35S promoter enhanced the GUS activity in response to thermospermine. Disruption experiments of each start codon of the SAC51 uORFs revealed that uORF4 and uORF6 whose start codon corresponds to the second methionine codon of uORF4 had an inhibitory effect on the main ORF translation while the other four uORFs rather had a stimulatory effect. The response of the 5' leader to thermospermine was retained after disruption of each one of six start codons of these uORFs but abolished by mutating both uORF4 and uORF6 start codons, suggesting the importance of the C-terminal sequence shared by these uORFs in the action of thermospermine. We introduced GUS fusions with 5' leaders of SAC51 family genes from other angiosperm species into Arabidopsis and found that all 5' leaders responsive to thermospermine, so far examined, contained these two conserved, and overlapping uORFs.
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25
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Fritz MA, Rosa S, Sicard A. Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology. Front Genet 2018; 9:478. [PMID: 30405690 PMCID: PMC6207588 DOI: 10.3389/fgene.2018.00478] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/26/2018] [Indexed: 01/23/2023] Open
Abstract
The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.
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Affiliation(s)
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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26
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Jia D, Gong X, Li M, Li C, Sun T, Ma F. Overexpression of a Novel Apple NAC Transcription Factor Gene, MdNAC1, Confers the Dwarf Phenotype in Transgenic Apple (Malus domestica). Genes (Basel) 2018; 9:E229. [PMID: 29702625 PMCID: PMC5977169 DOI: 10.3390/genes9050229] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
Plant height is an important trait for fruit trees. The dwarf characteristic is commonly associated with highly efficient fruit production, a major objective when breeding for apple (Malus domestica). We studied the function of MdNAC1, a novel NAC transcription factor (TF) gene in apple related to plant dwarfing. Localized primarily to the nucleus, MdNAC1 has transcriptional activity in yeast cells. Overexpression of the gene results in a dwarf phenotype in transgenic apple plants. Their reduction in size is manifested by shorter, thinner stems and roots, and a smaller leaf area. The transgenics also have shorter internodes and fewer cells in the stems. Levels of endogenous abscisic acid (ABA) and brassinosteroid (BR) are lower in the transgenic plants, and expression is decreased for genes involved in the biosynthesis of those phytohormones. All of these findings demonstrate that MdNAC1 has a role in plants dwarfism, probably by regulating ABA and BR production.
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Affiliation(s)
- Dongfeng Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Tingting Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
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27
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Moldován N, Tombácz D, Szűcs A, Csabai Z, Snyder M, Boldogkői Z. Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus. Front Microbiol 2018; 8:2708. [PMID: 29403453 PMCID: PMC5786565 DOI: 10.3389/fmicb.2017.02708] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
Third-generation sequencing is an emerging technology that is capable of solving several problems that earlier approaches were not able to, including the identification of transcripts isoforms and overlapping transcripts. In this study, we used long-read sequencing for the analysis of pseudorabies virus (PRV) transcriptome, including Oxford Nanopore Technologies MinION, PacBio RS-II, and Illumina HiScanSQ platforms. We also used data from our previous short-read and long-read sequencing studies for the comparison of the results and in order to confirm the obtained data. Our investigations identified 19 formerly unknown putative protein-coding genes, all of which are 5' truncated forms of earlier annotated longer PRV genes. Additionally, we detected 19 non-coding RNAs, including 5' and 3' truncated transcripts without in-frame ORFs, antisense RNAs, as well as RNA molecules encoded by those parts of the viral genome where no transcription had been detected before. This study has also led to the identification of three complex transcripts and 50 distinct length isoforms, including transcription start and end variants. We also detected 121 novel transcript overlaps, and two transcripts that overlap the replication origins of PRV. Furthermore, in silico analysis revealed 145 upstream ORFs, many of which are located on the longer 5' isoforms of the transcripts.
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Affiliation(s)
- Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Attila Szűcs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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28
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Abstract
Themospermine is a structural isomer of spermine and is present in some bacteria and most of plants. An Arabidopsis mutant, acaulis5 (acl5), that is defective in the biosynthesis of thermospermine displays excessive proliferation of xylem vessels with dwarfed growth. Recent studies using acl5 and its suppressor mutants that recover the growth without thermospermine have revealed that thermospermine plays a key role in the negative control of the proliferation of xylem vessels through enhancing translation of specific mRNAs that contain a conserved upstream open-reading-frame (uORF) in the 5' leader region.
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Affiliation(s)
- Taku Takahashi
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, kita-ku, 700-8530, Okayama, Japan.
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29
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Affiliation(s)
- Raili Ruonala
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;, ,
| | - Donghwi Ko
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;, ,
| | - Ykä Helariutta
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;, ,
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30
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Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
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Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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31
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Hayashi N, Sasaki S, Takahashi H, Yamashita Y, Naito S, Onouchi H. Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest. Nucleic Acids Res 2017. [PMID: 28637336 PMCID: PMC5587730 DOI: 10.1093/nar/gkx528] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Specific sequences of certain nascent peptides cause programmed ribosomal arrest during mRNA translation to control gene expression. In eukaryotes, most known regulatory arrest peptides are encoded by upstream open reading frames (uORFs) present in the 5′-untranslated region of mRNAs. However, to date, a limited number of eukaryotic uORFs encoding arrest peptides have been reported. Here, we searched for arrest peptide-encoding uORFs among Arabidopsis thaliana uORFs with evolutionarily conserved peptide sequences. Analysis of in vitro translation products of 22 conserved uORFs identified three novel uORFs causing ribosomal arrest in a peptide sequence-dependent manner. Stop codon-scanning mutagenesis, in which the effect of changing the uORF stop codon position on the ribosomal arrest was examined, and toeprint analysis revealed that two of the three uORFs cause ribosomal arrest during translation elongation, whereas the other one causes ribosomal arrest during translation termination. Transient expression assays showed that the newly identified arrest-causing uORFs exerted a strong sequence-dependent repressive effect on the expression of the downstream reporter gene in A. thaliana protoplasts. These results suggest that the peptide sequences of the three uORFs identified in this study cause ribosomal arrest in the uORFs, thereby repressing the expression of proteins encoded by the main ORFs.
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Affiliation(s)
- Noriya Hayashi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Shun Sasaki
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Chiba 263-8522, Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Satoshi Naito
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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32
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Ragni L, Greb T. Secondary growth as a determinant of plant shape and form. Semin Cell Dev Biol 2017; 79:58-67. [PMID: 28864343 DOI: 10.1016/j.semcdb.2017.08.050] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/26/2017] [Accepted: 08/28/2017] [Indexed: 02/06/2023]
Abstract
Plants are the primary producers of biomass on earth. As an almost stereotypic feature, higher plants generate continuously growing bodies mediated by the activity of different groups of stem cells, the meristems. Shoot and root thickening is one of the fundamental growth processes determining form and function of these bodies. Mediated by a group of cylindrical meristems located below organ surfaces, vascular and protective tissues are continuously generated in a highly plastic manner, a competence essential for the survival in an ever changing environment. Acknowledging the fundamental role of this process, which is overall designated as secondary growth, we discuss in this review our current knowledge about the evolution and molecular regulation of the vascular cambium. The cambium is the meristem responsible for the formation of wood and bast, the two types of vascular tissues important for long-distance transport of water and assimilates, respectively. Although regulatory patterns are only beginning to emerge, we show that cambium activity represents a highly rewarding model for studying cell fate decisions, tissue patterning and differentiation, which has experienced an outstanding phylogenetic diversification.
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Affiliation(s)
- Laura Ragni
- ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.
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33
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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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34
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Heo JO, Blob B, Helariutta Y. Differentiation of conductive cells: a matter of life and death. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:23-29. [PMID: 27794261 DOI: 10.1016/j.pbi.2016.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 05/26/2023]
Abstract
Two major conducting tissues in plants, phloem and xylem, are composed of highly specialized cell types adapted to long distance transport. Sieve elements (SEs) in the phloem display a thick cell wall, callose-rich sieve plates and low cytoplasmic density. SE differentiation is driven by selective autolysis combined with enucleation, after which the plasma membrane and some organelles are retained. By contrast, differentiation of xylem tracheary elements (TEs) involves complete clearance of the cellular components by programmed cell death followed by autolysis of the protoplast; this is accompanied by extensive deposition of lignin and cellulose in the cell wall. Emerging molecular data on TE and SE differentiation indicate a central role for NAC and MYB type transcription factors in both processes.
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Affiliation(s)
- Jung-Ok Heo
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Bernhard Blob
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Ykä Helariutta
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
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35
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Alabdallah O, Ahou A, Mancuso N, Pompili V, Macone A, Pashkoulov D, Stano P, Cona A, Angelini R, Tavladoraki P. The Arabidopsis polyamine oxidase/dehydrogenase 5 interferes with cytokinin and auxin signaling pathways to control xylem differentiation. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:997-1012. [PMID: 28199662 DOI: 10.1093/jxb/erw510] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In plants, the polyamines putrescine, spermidine, spermine (Spm), and thermospermine (Therm-Spm) participate in several physiological processes. In particular, Therm-Spm is involved in the control of xylem differentiation, having an auxin antagonizing effect. Polyamine oxidases (PAOs) are FAD-dependent enzymes involved in polyamine catabolism. In Arabidopsis, five PAOs are present, among which AtPAO5 catalyzes the back-conversion of Spm, Therm-Spm, and N1-acetyl-Spm to spermidine. In the present study, it is shown that two loss-of-function atpao5 mutants and a 35S::AtPAO5 Arabidopsis transgenic line present phenotypical differences from the wild-type plants with regard to stem and root elongation, differences that are accompanied by changes in polyamine levels and the number of xylem vessels. It is additionally shown that cytokinin treatment, which up-regulates AtPAO5 expression in roots, differentially affects protoxylem differentiation in 35S::AtPAO5, atpao5, and wild-type roots. Together with these findings, Therm-Spm biosynthetic genes, as well as auxin-, xylem-, and cytokinin-related genes (such as ACL5, SAMDC4, PIN1, PIN6, VND6, VND7, ATHB8, PHB, CNA, PXY, XTH3, XCP1, and AHP6) are shown to be differentially expressed in the various genotypes. These data suggest that AtPAO5, being involved in the control of Therm-Spm homeostasis, participates in the tightly controlled interplay between auxin and cytokinins that is necessary for proper xylem differentiation.
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Affiliation(s)
| | - Abdellah Ahou
- Department of Sciences, University 'ROMA TRE', Rome, Italy
| | | | | | - Alberto Macone
- Department of Biochemical Sciences 'A. Rossi Fanelli', University of Rome 'La Sapienza', Rome, Italy
| | - Dimitre Pashkoulov
- Società Agricola Floramiata Servizi srl, 53025 Piancastagnaio, Siena, Italy
| | - Pasquale Stano
- Department of Sciences, University 'ROMA TRE', Rome, Italy
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36
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Barra-Jiménez A, Ragni L. Secondary development in the stem: when Arabidopsis and trees are closer than it seems. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:145-151. [PMID: 28013083 DOI: 10.1016/j.pbi.2016.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
Secondary growth, the increase in girth of plant organs, is primarily driven by the vascular and cork cambium. In perennial dicotyledons and gymnosperms, it represents a major source of biomass accumulation in the form of wood. However, the molecular framework underlying secondary growth is largely based on studies in the annual herbaceous plant Arabidopsis thaliana. In this review, we will focus on a selection of major regulators of stem secondary growth, which have recently been shown to play a role in woody species. In particular, we will focus on thermospermine and its bivalent role in controlling xylem differentiation and cell proliferation and we will highlight the contributions of the different LRR-Receptor-Like Kinase signaling hubs.
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Affiliation(s)
- Azahara Barra-Jiménez
- ZMBP-Center for Plant Molecular Biology, Auf der Morgenstelle 32, 72070 Tübingen, Germany
| | - Laura Ragni
- ZMBP-Center for Plant Molecular Biology, Auf der Morgenstelle 32, 72070 Tübingen, Germany.
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37
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Yamamoto M, Takahashi T. Thermospermine enhances translation of SAC51 and SACL1 in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1276685. [PMID: 28045577 PMCID: PMC5289521 DOI: 10.1080/15592324.2016.1276685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 05/25/2023]
Abstract
The excessive xylem phenotype of acaulis5 (acl5), an Arabidopsis mutant defective in the synthesis of thermospermine, indicates that thermospermine is required for negative regulation of xylem differentiation. SAC51 was identified from a dominant suppressor of acl5, sac51-d, and encodes a basic helix-loop-helix (bHLH) protein. sac51-d has a premature termination codon in one of upstream open-reading frames (uORFs) of the SAC51 mRNA that is conserved among the SAC51 family members. Thermospermine may act to bypass the inhibitory effect of the uORF on main ORF translation. Another suppressor, sac57-d, also has a mutation in the conserved uORF of SACL3, a member of the SAC51 family. On the other hand, the double knockout of SAC51 and SACL3 is insensitive to thermospermine, suggesting their key role in the response to thermospermine. However, we found that thermospermine enhances mRNA translation of SAC51 and SACL1 but not of SACL2 and SACL3. Taken together with recent findings from other groups, we propose a mechanism by which thermospermine diffused from xylem precursor cells acts non-cell-autonomously to restrict their proliferation.
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Affiliation(s)
- Mai Yamamoto
- Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka, Okayama, Japan
| | - Taku Takahashi
- Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka, Okayama, Japan
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38
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Etchells JP, Turner SR. Realizing pipe dreams - a detailed picture of vascular development. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1-4. [PMID: 28013229 PMCID: PMC5183087 DOI: 10.1093/jxb/erw482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- J Peter Etchells
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK,
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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39
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Abstract
Vascular tissue, comprising xylem and phloem, is responsible for the transport of water and nutrients throughout the plant body. Such tissue is continually produced from stable populations of stem cells, specifically the procambium during primary growth and the cambium during secondary growth. As the majority of plant biomass is produced by the cambium, there is an obvious demand for an understanding of the genetic mechanisms that control the rate of vascular cell division. Moreover, wood is an industrially important product of the cambium, and research is beginning to uncover similar mechanisms in trees such as poplar. This review focuses upon recent work that has identified the major molecular pathways that regulate procambial and cambial activity.
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Affiliation(s)
- Liam Campbell
- University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon Turner
- University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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40
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Guerrero-González MDLL, Ortega-Amaro MA, Juárez-Montiel M, Jiménez-Bremont JF. Arabidopsis Polyamine oxidase-2 uORF is required for downstream translational regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:381-390. [PMID: 27526386 DOI: 10.1016/j.plaphy.2016.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 05/10/2023]
Abstract
In eukaryotic mRNAs, small upstream open reading frames (uORFs) located in the 5'-untranslated region control the translation of the downstream main ORF. Polyamine oxidase (PAO) enzymes catalyze the oxidation of higher polyamines such as spermidine and spermine, and therefore contribute to the maintenance of intracellular polyamine content and to the regulation of physiological processes through their catabolic products. Recently, we reported that the Arabidopsis thaliana Polyamine Oxidase 2 (AtPAO2) is post-transcriptionally regulated by its 5'-UTR region through an uORF. In the present study, we analyzed whether the translation of the uORF is needed for the translational repression of the main ORF, and whether the inactivation of the uORF had an effect on the translational control mediated by polyamines. To this aim, we generated diverse single mutations in the uORF sequence; these mutant 5'-UTRs were fused to the GUS reporter gene, and tested in onion monolayer cells and A. thaliana transgenic seedlings. Removal of the start codon or introduction of a premature stop codon in the AtPAO2 uORF sequence abolished the negative regulation of the GUS expression exerted by the wild-type AtPAO2 uORF. An artificial uORF (32 amino acids in length) generated by the addition of a single nucleotide in AtPAO2 uORF proved to be less repressive than the wild-type uORF. Thus, our findings suggest that translation of the AtPAO2 uORF is necessary for the translational repression of the main ORF.
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Affiliation(s)
| | - María Azucena Ortega-Amaro
- Instituto Potosino de Investigación Científica y Tecnológica AC, División de Biología Molecular, San Luis Potosí, Mexico
| | - Margarita Juárez-Montiel
- Instituto Potosino de Investigación Científica y Tecnológica AC, División de Biología Molecular, San Luis Potosí, Mexico
| | - Juan Francisco Jiménez-Bremont
- Instituto Potosino de Investigación Científica y Tecnológica AC, División de Biología Molecular, San Luis Potosí, Mexico.
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41
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Gao X, Walworth AE, Mackie C, Song GQ. Overexpression of blueberry FLOWERING LOCUS T is associated with changes in the expression of phytohormone-related genes in blueberry plants. HORTICULTURE RESEARCH 2016; 3:16053. [PMID: 27818778 PMCID: PMC5080838 DOI: 10.1038/hortres.2016.53] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 05/08/2023]
Abstract
Flowering locus T (FT) is a primary integrator in the regulation of plant flowering. Overexpressing a blueberry (Vaccinium corymbosum L.) FT gene (VcFT) (herein VcFT-OX) resulted in early flowering and dwarfing in 'Aurora' plants (herein 'VcFT-Aurora'). In this study, we found that VcFT-OX reduced shoot regeneration from leaf explants. To investigate the potential roles of the phytohormone pathway genes associated with VcFT-OX, differentially expressed (DE) genes in leaf tissues of 'VcFT-Aurora' plants were annotated and analyzed using non-transgenic 'Aurora' plants as a control. Three DE floral genes, including the blueberry SUPPRESSOR of Overexpression of constans 1 (VcSOC1) (gibberellin related), Abscisic acid responsive elements-binding factor 2 (VcABF2) and protein related to ABI3/VP1 (VcABI3/VP1) (ethylene-related), are present under both the phytohormone-responsive and the dwarfing-related Gene Ontology terms. The gene networks of the DE genes overall showed the molecular basis of the multifunctional aspects of VcFT overexpression beyond flowering promotion and suggested that phytohormone changes could be signaling molecules with important roles in the phenotypic changes driven by VcFT-OX.
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Affiliation(s)
- Xuan Gao
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
- Key Laboratory for the Conservation and Utilization of Important Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Aaron E Walworth
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - Charity Mackie
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-qing Song
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
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Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proc Natl Acad Sci U S A 2016; 113:E7126-E7135. [PMID: 27791167 DOI: 10.1073/pnas.1614788113] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
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43
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Ohashi-Ito K, Fukuda H. Functional mechanism of bHLH complexes during early vascular development. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:42-47. [PMID: 27314622 DOI: 10.1016/j.pbi.2016.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 05/27/2023]
Abstract
The vascular system spreads throughout the plant body. This highly organized network contains several types of cells. Vascular cell development is initiated during embryogenesis, and then vascular cells proliferate, form a vascular pattern, and commit to specific cell fates. Recent molecular genetics and modeling approaches have increased our understanding of the molecular mechanisms underlying early vascular development. Early events during vascular development are tightly linked and controlled by transcriptional complexes consisting of LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS5 (TMO5) families. The role of LHW-TMO5 is tightly coupled with biosynthesis and/or signaling of phytohormones such as auxin and cytokinin. In this review, we discuss the regulatory network mediated by LHW-TMO5 during early vascular development.
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Affiliation(s)
- Kyoko Ohashi-Ito
- Department Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Hiroo Fukuda
- Department Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan.
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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45
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Cai Q, Fukushima H, Yamamoto M, Ishii N, Sakamoto T, Kurata T, Motose H, Takahashi T. The SAC51 Family Plays a Central Role in Thermospermine Responses in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:1583-92. [PMID: 27388339 DOI: 10.1093/pcp/pcw113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/09/2016] [Indexed: 05/09/2023]
Abstract
The acaulis5 (acl5) mutant of Arabidopsis thaliana is defective in the biosynthesis of thermospermine and shows a dwarf phenotype associated with excess xylem differentiation. SAC51 was identified from a dominant suppressor of acl5, sac51-d, and encodes a basic helix-loop-helix protein. The sac51-d mutant has a premature termination codon in an upstream open reading frame (uORF) that is conserved among all four members of the SAC51 family, SAC51 and SACL1-SACL3 This suggests that thermospermine cancels the inhibitory effect of the uORF in main ORF translation. Another suppressor, sac57-d, has a mutation in the conserved uORF of SACL3 To define further the function of the SAC51 family in the thermospermine response, we analyzed T-DNA insertion mutants of each gene. Although sacl1-1 may not be a null allele, the quadruple mutant showed a semi-dwarf phenotype but with an increased level of thermospermine and decreased sensitivity to exogenous thermospermine that normally represses xylem differentiation. The sac51-1 sacl3-1 double mutant was also insensitive to thermospermine. These results suggest that SAC51 and SACL3 play a key role in thermospermine-dependent negative control of thermospermine biosynthesis and xylem differentiation. Using 5' leader-GUS (β-glucuronidase) fusion constructs, however, we detected a significant enhancement of the GUS activity by thermospermine only in SAC51 and SACL1 constructs. Furthermore, while acl5-1 sac51-1 showed the acl5 dwarf phenotype, acl5-1 sacl3-1 exhibited an extremely tiny-plant phenotype. These results suggest a complex regulatory network for the thermospermine response in which SAC51 and SACL3 function in parallel pathways.
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Affiliation(s)
- Qingqing Cai
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hiroko Fukushima
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Mai Yamamoto
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Nami Ishii
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Tomoaki Sakamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hiroyasu Motose
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Taku Takahashi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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46
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Wang Y, He J, Yang L, Wang Y, Chen W, Wan S, Chu P, Guan R. Fine mapping of a major locus controlling plant height using a high-density single-nucleotide polymorphism map in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1479-91. [PMID: 27147069 DOI: 10.1007/s00122-016-2718-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/19/2016] [Indexed: 05/08/2023]
Abstract
A saturated map was constructed using SNP markers to fine-map a Brassica napus dominant locus for dwarf mutant onto a 152-kb interval of chromosome A09 containing 14 genes. Major dwarf loci in crops may play important roles in crop improvement and developmental genetics. The present study investigated and fine-mapped a Brassica napus dwarf-dominant locus BnDWF1. Plants carrying the BnDWF1 locus in populations derived from 'zhongshuang11' and Bndwf1 have deep-green leaves and dwarf architecture that differ sharply from tall plants with normal green leaves. BnDWF1, as a major locus controlling plant height, showed a very high heritability (0.91-0.95). To map this locus, a high-density single-nucleotide polymorphism map was constructed, and the BnDWF1 locus was mapped at an interval between single-nucleotide polymorphism markers, M19704 and M19695, on linkage group A09 of B. napus, with five co-segregating single-nucleotide polymorphism markers. Furthermore, fine mapping narrowed the interval harboring BnDWF1 to 152 kb in length in B. napus. This interval contains 14 annotated or predicted genes, seven of which are candidates responsible for the dwarf trait. This study provides an effective foundation for the study of plant height regulation and plant type breeding in B. napus.
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Affiliation(s)
- Yankun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Jianbo He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Li Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Yu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Wenjing Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Shubei Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China.
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47
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Daneva A, Gao Z, Van Durme M, Nowack MK. Functions and Regulation of Programmed Cell Death in Plant Development. Annu Rev Cell Dev Biol 2016; 32:441-468. [PMID: 27298090 DOI: 10.1146/annurev-cellbio-111315-124915] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Programmed cell death (PCD) is a collective term for diverse processes causing an actively induced, tightly controlled cellular suicide. PCD has a multitude of functions in the development and health of multicellular organisms. In comparison to intensively studied forms of animal PCD such as apoptosis, our knowledge of the regulation of PCD in plants remains limited. Despite the importance of PCD in plant development and as a response to biotic and abiotic stresses, the complex molecular networks controlling different forms of plant PCD are only just beginning to emerge. With this review, we provide an update on the considerable progress that has been made over the last decade in our understanding of PCD as an inherent part of plant development. We highlight both functions of developmental PCD and central aspects of its molecular regulation.
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Affiliation(s)
- Anna Daneva
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Zhen Gao
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Matthias Van Durme
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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48
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Wang Y, Xiao X, Wang X, Zeng J, Kang H, Fan X, Sha L, Zhang H, Zhou Y. RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.). Int J Biol Sci 2016; 12:653-66. [PMID: 27194943 PMCID: PMC4870709 DOI: 10.7150/ijbs.14577] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/15/2016] [Indexed: 11/05/2022] Open
Abstract
The dwarfing mechanism of Rht-dp in dwarf Polish wheat (DPW) is unknown. Each internode of DPW was significantly shorter than it in high Polish wheat (HPW), and the dwarfism was insensitive to photoperiod, abscisic acid (ABA), gibberellin (GA), cytokinin (CK), auxin and brassinolide (BR). To understand the mechanism, three sets of transcripts, DPW, HPW, and a chimeric set (a combination of DPW and HPW), were constructed using RNA sequencing (RNA-Seq). Based on the chimeric transcripts, 2,446 proteins were identified using isobaric tags for relative and absolute quantification (iTRAQ). A total of 108 unigenes and 12 proteins were considered as dwarfism-related differentially expressed genes (DEGs) and differentially expressed proteins (DEPs), respectively. Among of these DEGs and DEPs, 6 DEGs and 6 DEPs were found to be involved in flavonoid and S-adenosyl-methionine (SAM) metabolisms; 5 DEGs and 3 DEPs were involved in cellulose metabolism, cell wall plasticity and cell expansion; 2 DEGs were auxin transporters; 2 DEPs were histones; 1 DEP was a peroxidase. These DEGs and DEPs reduced lignin and cellulose contents, increased flavonoid content, possibly decreased S-adenosyl-methionine (SAM) and polyamine contents and increased S-adenosyl-L-homocysteine hydrolase (SAHH) content in DPW stems, which could limit auxin transport and reduce extensibility of the cell wall, finally limited cell expansion (the cell size of DPW was significantly smaller than HPW cells) and caused dwarfism in DPW.
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Affiliation(s)
- Yi Wang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xue Xiao
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xiaolu Wang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Jian Zeng
- 2. College of Resources, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Houyang Kang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xing Fan
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Lina Sha
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Haiqin Zhang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yonghong Zhou
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
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49
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Chemical control of xylem differentiation by thermospermine, xylemin, and auxin. Sci Rep 2016; 6:21487. [PMID: 26879262 PMCID: PMC4754900 DOI: 10.1038/srep21487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/25/2016] [Indexed: 12/14/2022] Open
Abstract
The xylem conducts water and minerals from the root to the shoot and provides mechanical strength to the plant body. The vascular precursor cells of the procambium differentiate to form continuous vascular strands, from which xylem and phloem cells are generated in the proper spatiotemporal pattern. Procambium formation and xylem differentiation are directed by auxin. In angiosperms, thermospermine, a structural isomer of spermine, suppresses xylem differentiation by limiting auxin signalling. However, the process of auxin-inducible xylem differentiation has not been fully elucidated and remains difficult to manipulate. Here, we found that an antagonist of spermidine can act as an inhibitor of thermospermine biosynthesis and results in excessive xylem differentiation, which is a phenocopy of a thermospermine-deficient mutant acaulis5 in Arabidopsis thaliana. We named this compound xylemin owing to its xylem-inducing effect. Application of a combination of xylemin and thermospermine to wild-type seedlings negates the effect of xylemin, whereas co-treatment with xylemin and a synthetic proauxin, which undergoes hydrolysis to release active auxin, has a synergistic inductive effect on xylem differentiation. Thus, xylemin may serve as a useful transformative chemical tool not only for the study of thermospermine function in various plant species but also for the control of xylem induction and woody biomass production.
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50
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Hu Q, Merchante C, Stepanova AN, Alonso JM, Heber S. Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana. IEEE Trans Nanobioscience 2016; 15:148-57. [PMID: 26886998 DOI: 10.1109/tnb.2016.2516950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Upstream open reading frames (uORFs) are open reading frames that occur within the 5' UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes. It is believed that translated uORFs reduce the translational efficiency of the main coding region. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana. Our approach identified 5360 potentially translated uORFs in 2051 genes. GO terms enriched in genes with translated uORFs include catalytic activity, binding, transferase activity, phosphotransferase activity, kinase activity, and transcription regulator activity. The reported uORFs occur with a higher frequency in multi-isoform genes, and some uORFs are affected by alternative transcript start sites or alternative splicing events. Association rule mining revealed sequence features associated with the translation status of the uORFs. We hypothesize that uORF translation is a complex process that might be regulated by multiple factors. The identified uORFs are available online at:https://www.dropbox.com/sh/zdutupedxafhly8/AABFsdNR5zDfiozB7B4igFcja?dl=0. This paper is the extended version of our research presented at ISBRA 2015.
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