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Park J, Giudicatti AJ, Bader ZE, Han MK, Møller C, Arce AL, Xu ZY, Yang SW, Manavella PA, Yun DJ. The HOS15-HDA9 complex associates with HYL1 to modulate miRNA expression in response to ABA signaling. Plant Cell 2023:7169302. [PMID: 37195876 PMCID: PMC10396366 DOI: 10.1093/plcell/koad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023]
Abstract
The regulation of microRNA (miRNA) biogenesis is crucial for maintaining plant homeostasis under biotic and abiotic stress. The crosstalk between the RNA polymerase II (Pol-II) complex and the miRNA processing machinery has emerged as a central hub modulating transcription and co-transcriptional processing of primary miRNA transcripts (pri-miRNAs). However, it remains unclear how miRNA-specific transcriptional regulators recognize MIRNA loci. Here, we show that the Arabidopsis (Arabidopsis thaliana) HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15 (HOS15)-HISTONE DEACETYLASE9 (HDA9) complex is a conditional suppressor of miRNA biogenesis, particularly in response to ABA. When treated with ABA, hos15/hda9 mutants show enhanced transcription of pri-miRNAs that is accompanied by increased processing, leading to over-accumulation of a set of mature miRNAs. Moreover, upon recognition of the nascent pri-miRNAs, the ABA-induced recruitment of the HOS15-HDA9 complex to MIRNA loci is guided by HYPONASTIC LEAVES 1 (HYL1). The HYL1-dependent recruitment of the HOS15-HDA9 complex to MIRNA loci suppresses expression of MIRNAs and processing of pri-miRNA. Most importantly, our findings indicate that nascent pri-miRNAs serve as scaffolds for recruiting transcriptional regulators, specifically to MIRNA loci. This indicates that RNA molecules can act as regulators of their own expression by causing a negative feedback loop that turns off their transcription, providing a self-buffering system.
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Affiliation(s)
- Junghoon Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Zein Eddin Bader
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Min Kyun Han
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Christian Møller
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Muchut RJ, Calloni RD, Arias DG, Arce AL, Iglesias AA, Guerrero SA. Elucidating carbohydrate metabolism in Euglena gracilis: Reverse genetics-based evaluation of genes coding for enzymes linked to paramylon accumulation. Biochimie 2021; 184:125-131. [PMID: 33675853 DOI: 10.1016/j.biochi.2021.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/24/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Euglena gracilis is a eukaryotic single-celled and photosynthetic organism grouped under the kingdom Protista. This phytoflagellate can accumulate the carbon photoassimilate as a linear β-1,3-glucan chain called paramylon. This storage polysaccharide can undergo degradation to provide glucose units to obtain ATP and reducing power both in aerobic and anaerobic growth conditions. Our group has recently characterized an essential enzyme for accumulating the polysaccharide, the UDP-glucose pyrophosphorylase (Biochimie vol 154, 2018, 176-186), which catalyzes the synthesis of UDP-glucose (the substrate for paramylon synthase). Additionally, the identification of nucleotide sequences coding for putative UDP-sugar pyrophosphorylases suggests the occurrence of an alternative source of UDP-glucose. In this study, we demonstrate the active involvement of both pyrophosphorylases in paramylon accumulation. Using techniques of single and combined knockdown of transcripts coding for these proteins, we evidenced a substantial decrease in the polysaccharide synthesis from 39 ± 7 μg/106 cells determined in the control at day 21st of growth. Thus, the paramylon accumulation in Euglena gracilis cells decreased by 60% and 30% after a single knockdown of the expression of genes coding for UDP-glucose pyrophosphorylase and UDP-sugar pyrophosphorylase, respectively. Besides, the combined knockdown of both genes resulted in a ca. 65% reduction in the level of the storage polysaccharide. Our findings indicate the existence of a physiological dependence between paramylon accumulation and the partitioning of sugar nucleotides into other metabolic routes, including the Leloir pathway's functionality in Euglena gracilis.
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Affiliation(s)
- Robertino J Muchut
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Rodrigo D Calloni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Diego G Arias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina.
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3
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Cambiagno DA, Giudicatti AJ, Arce AL, Gagliardi D, Li L, Yuan W, Lundberg DS, Weigel D, Manavella PA. HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. Mol Plant 2021; 14:426-439. [PMID: 33385584 DOI: 10.1016/j.molp.2020.12.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/23/2023]
Abstract
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.
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Affiliation(s)
- Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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Giudicatti AJ, Tomassi AH, Manavella PA, Arce AL. Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover. Plants (Basel) 2021; 10:plants10020267. [PMID: 33573197 PMCID: PMC7911489 DOI: 10.3390/plants10020267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.
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5
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Tomassi AH, Re DA, Romani F, Cambiagno DA, Gonzalo L, Moreno JE, Arce AL, Manavella PA. The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity. Plant Physiol 2020; 184:316-329. [PMID: 32636339 PMCID: PMC7479909 DOI: 10.1104/pp.20.00258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2020] [Indexed: 05/04/2023]
Abstract
In plants, small RNAs are loaded into ARGONAUTE (AGO) proteins to fulfill their regulatory functions. MicroRNAs (miRNAs), one of the most abundant classes of endogenous small RNAs, are preferentially loaded into AGO1. Such loading, long believed to happen exclusively in the cytoplasm, was recently proposed to also occur in the nucleus. Here, we identified CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9 (CARP9), a nuclear-localized, intrinsically disordered protein, as a factor promoting miRNA activity in Arabidopsis (Arabidopsis thaliana). Mutations in the CARP9-encoding gene led to a mild reduction of miRNAs levels, impaired gene silencing, and characteristic morphological defects, including young leaf serration and altered flowering time. Intriguingly, we found that CARP9 was able to interact with HYPONASTIC LEAVES1 (HYL1), but not with other proteins of the miRNA biogenesis machinery. In the same way, CARP9 appeared to interact with mature miRNA, but not with primary miRNA, positioning it after miRNA processing in the miRNA pathway. CARP9 was also able to interact with AGO1, promoting its interaction with HYL1 to facilitate miRNA loading in AGO1. Plants deficient in CARP9 displayed reduced levels of AGO1-loaded miRNAs, partial retention of miRNA in the nucleus, and reduced levels of AGO1. Collectively, our data suggest that CARP9 might modulate HYL1-AGO1 cross talk, acting as a scaffold for the formation of a nuclear post-primary miRNA-processing complex that includes at least HYL1, AGO1, and HEAT SHOCK PROTEIN 90. In such a complex, CARP9 stabilizes AGO1 and mature miRNAs, allowing the proper loading of miRNAs in the effector complex.
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Affiliation(s)
- Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Facundo Romani
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Lucía Gonzalo
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Javier E Moreno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
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6
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Choi SW, Ryu MY, Viczián A, Jung HJ, Kim GM, Arce AL, Achkar NP, Manavella P, Dolde U, Wenkel S, Molnár A, Nagy F, Cho SK, Yang SW. Light Triggers the miRNA-Biogenetic Inconsistency for De-etiolated Seedling Survivability in Arabidopsis thaliana. Mol Plant 2020; 13:431-445. [PMID: 31678531 DOI: 10.1016/j.molp.2019.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/17/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels. However, the levels of most miRNAs do not notably increase in response to light. To reconcile this inconsistency, we demonstrated that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, these data suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions.
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Affiliation(s)
- Suk Won Choi
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Moon Young Ryu
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - András Viczián
- Institute of Plant Biology, Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Hyun Ju Jung
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Gu Min Kim
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (IAL) Centro Científico Tecnológico Santa Fe (CCT), Santa Fe, Argentina
| | - Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (IAL) Centro Científico Tecnológico Santa Fe (CCT), Santa Fe, Argentina
| | - Pablo Manavella
- Instituto de Agrobiotecnología del Litoral (IAL) Centro Científico Tecnológico Santa Fe (CCT), Santa Fe, Argentina
| | - Ulla Dolde
- Laboratoire de Recherche en Sciences Végétales, 24, chemin de Borde-Rouge, BP 42617 Auzeville, Castanet-Tolosan 31326, France
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Copenhagen 1871, Denmark
| | - Attila Molnár
- Institute of Molecular Plant Sciences, School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Seok Keun Cho
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Copenhagen 1871, Denmark.
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7
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Ré DA, Cambiagno DA, Arce AL, Tomassi AH, Giustozzi M, Casati P, Ariel FD, Manavella PA. CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants. Mol Plant 2020; 13:72-87. [PMID: 31606467 DOI: 10.1016/j.molp.2019.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.
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Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Marisol Giustozzi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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8
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Ré DA, Lang PLM, Yones C, Arce AL, Stegmayer G, Milone D, Manavella PA. Alternative use of miRNA-biogenesis co-factors in plants at low temperatures. Development 2019; 146:dev.172932. [PMID: 30760482 DOI: 10.1242/dev.172932] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/04/2019] [Indexed: 01/31/2023]
Abstract
Plants use molecular mechanisms to sense temperatures, trigger quick adaptive responses and thereby cope with environmental changes. MicroRNAs (miRNAs) are key regulators of plant development under such conditions. The catalytic action of DICER LIKE 1 (DCL1), in conjunction with HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE), produces miRNAs from double-stranded RNAs. As plants lack a stable internal temperature to which enzymatic reactions could be optimized during evolution, reactions such as miRNA processing have to be adjusted to fluctuating environmental temperatures. Here, we report that with decreasing ambient temperature, the plant miRNA biogenesis machinery becomes more robust, producing miRNAs even in the absence of the key DCL1 co-factors HYL1 and SE. This reduces the morphological and reproductive defects of se and hyl1 mutants, restoring seed production. Using small RNA-sequencing and bioinformatics analyses, we have identified specific miRNAs that become HYL1/SE independent for their production in response to temperature decrease. We found that the secondary structure of primary miRNAs is key for this temperature recovery. This finding may have evolutionary implications as a potential adaptation-driving mechanism to a changing climate.
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Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Patricia L M Lang
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina.,Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence [sinc(i)], Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence [sinc(i)], Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Diego Milone
- Research Institute for Signals, Systems and Computational Intelligence [sinc(i)], Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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Göbel U, Arce AL, He F, Rico A, Schmitz G, de Meaux J. Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. Genome Biol Evol 2018; 10:1403-1415. [PMID: 29788048 PMCID: PMC6007786 DOI: 10.1093/gbe/evy095] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/23/2022] Open
Abstract
The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.
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Affiliation(s)
- Ulrike Göbel
- Botanical Institute, University of Cologne, Germany
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), 3000 Santa Fe, Argentina
| | - Fei He
- Botanical Institute, University of Cologne, Germany
| | - Alain Rico
- Thermo Fisher Scientific, Villebon-sur-Yvette, France
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Achkar NP, Cho SK, Poulsen C, Arce AL, Re DA, Giudicatti AJ, Karayekov E, Ryu MY, Choi SW, Harholt J, Casal JJ, Yang SW, Manavella PA. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Dev Cell 2018; 46:236-247.e6. [PMID: 30016624 DOI: 10.1016/j.devcel.2018.06.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/14/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
Abstract
Light is the most influential environmental stimulus for plant growth. In response to deficient light, plants reprogram their development to adjust their growth in search for a light source. A fine reprogramming of gene expression orchestrates this adaptive trait. Here we show that plants alter microRNA (miRNA) biogenesis in response to light transition. When plants suffer an unusual extended period of light deprivation, the miRNA biogenesis factor HYPONASTIC LEAVES 1 (HYL1) is degraded but an inactive pool of phosphorylated protein remains stable inside the nucleus. Degradation of HYL1 leads to the release of gene silencing, triggering a proper response to dark and shade. Upon light restoration, a quick dephosphorylation of HYL1 leads to the reactivation of miRNA biogenesis and a switch toward a developmental program that maximizes the light uptake. Our findings define a unique and fast regulatory mechanism controlling the plant silencing machinery during plant light response.
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Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | | | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Elizabeth Karayekov
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina
| | - Moon Young Ryu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Suk Won Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jesper Harholt
- Carlsberg Research Laboratory, Copenhagen V 1799, Denmark
| | - Jorge J Casal
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina; Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires 1405, Argentina
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina.
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He F, Arce AL, Schmitz G, Koornneef M, Novikova P, Beyer A, de Meaux J. The Footprint of Polygenic Adaptation on Stress-ResponsiveCis-Regulatory Divergence in theArabidopsis Genus. Mol Biol Evol 2016; 33:2088-101. [DOI: 10.1093/molbev/msw096] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Abstract
Transcription factors are clue elements in the regulation of signal transduction pathways in living organisms. These proteins are able to recognize and bind specific sequences in the promoter regions of their targets and subsequently activate or repress entire metabolic or developmental processes. About 1500 TFs were informatically identified in plants, analysis mainly based in the presence of DNA-binding domains in the translated sequences. However, only a few of these 1500 were functionally characterized and clearly classified as TFs. Among these, several seem to be powerful biotechnological tools in order to improve agronomic crops via the obtaining of transgenic plants or as molecular markers. Such TFs have become the objects of patents presentations in the whole world. The assigned uses present a variety of purposes including the improvement in yield, abiotic and biotic stresses tolerances as well as a combination of them. Some examples are commented in the present overview. Most of these TFs confer to transgenic plants complex phenotypes due to a combination of different regulated pathways. In this sense, the use of inducible promoters instead of constitutive ones seems in some cases to be useful to limit the changed phenotype to the desired one, avoiding lateral effects. None of these TFs was converted up to now in a market product since time-consuming experiments and regulation permits are required to arrive to such point. Moreover, a considerable money investment must be done, not justified in all cases. However, it is likely that these molecules will become in the near future the first choice for breeders since it was demonstrated that TFs are very efficient conferring desired traits to transgenic plants. Additionally, for the public perception the over or ectopic expression of a plant gene should be more accepted than the use of molecules from other species.
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Affiliation(s)
- Agustin L Arce
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, CONICET, CC 242 Ciudad Universitaria, 3000, Santa Fe, Argentina
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