1
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Marmisolle FE, Borniego MB, Cambiagno DA, Gonzalo L, García ML, Manavella PA, Hernández C, Reyes CA. Citrus psorosis virus 24K protein inhibits the processing of miRNA precursors by interacting with components of the biogenesis machinery. Microbiol Spectr 2024:e0351323. [PMID: 38785434 DOI: 10.1128/spectrum.03513-23] [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: 10/31/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Sweet orange (Citrus sinensis) is one of the most important fruit crops worldwide. Virus infections in this crop can interfere with cellular processes, causing dramatic economic losses. By performing RT-qPCR analyses, we demonstrated that citrus psorosis virus (CPsV)-infected orange plants exhibited higher levels of unprocessed microRNA (miRNA) precursors than healthy plants. This result correlated with the reported reduction of mature miRNAs species. The protein 24K, the CPsV suppressor of RNA silencing (VSR), interacts with miRNA precursors in vivo. Thus, this protein becomes a candidate responsible for the increased accumulation of unprocessed miRNAs. We analyzed 24K RNA-binding and protein-protein interaction domains and described patterns of its subcellular localization. We also showed that 24K colocalizes within nuclear D-bodies with the miRNA biogenesis proteins DICER-LIKE 1 (DCL1), HYPONASTIC LEAVES 1 (HYL1), and SERRATE (SE). According to the results of bimolecular fluorescence complementation and co-immunoprecipitation assays, the 24K protein interacts with HYL1 and SE. Thus, 24K may inhibit miRNA processing in CPsV-infected citrus plants by direct interaction with the miRNA processing complex. This work contributes to the understanding of how a virus can alter the regulatory mechanisms of the host, particularly miRNA biogenesis and function.IMPORTANCESweet oranges can suffer from disease symptoms induced by virus infections, thus resulting in drastic economic losses. In sweet orange plants, CPsV alters the accumulation of some precursors from the regulatory molecules called miRNAs. This alteration leads to a decreased level of mature miRNA species. This misregulation may be due to a direct association of one of the viral proteins (24K) with miRNA precursors. On the other hand, 24K may act with components of the cell miRNA processing machinery through a series of predicted RNA-binding and protein-protein interaction domains.
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Affiliation(s)
- Facundo E Marmisolle
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - María B Borniego
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Damián 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, Santa Fe, Argentina
| | - Lucia Gonzalo
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - María L García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, 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, Santa Fe, Argentina
| | - Carmen Hernández
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
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2
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Chen W, Wang J, Wang Z, Zhu T, Zheng Y, Hawar A, Chang Y, Wang X, Li D, Wang G, Yang W, Zhao Y, Chen D, Yuan YA, Sun B. Capture of regulatory factors via CRISPR-dCas9 for mechanistic analysis of fine-tuned SERRATE expression in Arabidopsis. NATURE PLANTS 2024; 10:86-99. [PMID: 38168608 DOI: 10.1038/s41477-023-01575-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/29/2023] [Indexed: 01/05/2024]
Abstract
SERRATE (SE) plays an important role in many biological processes and under biotic stress resistance. However, little about the control of SE has been clarified. Here we present a method named native chromatin-associated proteome affinity by CRISPR-dCas9 (CASPA-dCas9) to holistically capture native regulators of the SE locus. Several key regulatory factors including PHYTOCHROME RAPIDLY REGULATED 2 (PAR2), WRKY DNA-binding protein 19 (WRKY19) and the MYB-family protein MYB27 of SE are identified. MYB27 recruits the long non-coding RNA-PRC2 (SEAIR-PRC2) complex for H3K27me3 deposition on exon 1 of SE and subsequently represses SE expression, while PAR2-MYB27 interaction inhibits both the binding of MYB27 on the SE promoter and the recruitment of SEAIR-PRC2 by MYB27. The interaction between PAR2 and MYB27 fine-tunes the SE expression level at different developmental stages. In addition, PAR2 and WRKY19 synergistically promote SE expression for pathogen resistance. Collectively, our results demonstrate an efficient method to capture key regulators of target genes and uncover the precise regulatory mechanism for SE.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
| | - Jingyi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zijing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yuchen Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Amangul Hawar
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yongsheng Chang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dongbao Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guangling Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wen Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanjie Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yuren Adam Yuan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Bo Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
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3
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Zhao G, Niu J, Hai Z, Li T, Xie D, Li Y, Qi Y. Peptidyl-prolyl isomerase Cyclophilin71 promotes SERRATE phase separation and miRNA processing in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2305244120. [PMID: 37639607 PMCID: PMC10483624 DOI: 10.1073/pnas.2305244120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
MicroRNAs (miRNAs) play an important role in gene regulation. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts by the Dicing complex that contains Dicer-like 1 (DCL1), SERRATE (SE), and Hyponastic Leaves 1 (HYL1). The Dicing complex can form nuclear dicing bodies (D-bodies) through SE phase separation. Here, we report that Cyclophilin71 (CYP71), a peptidyl-prolyl isomerase (PPIase), positively regulates miRNA processing. We show that CYP71 directly interacts with SE and enhances its phase separation, thereby promoting the formation of D-body and increasing the activity of the Dicing complex. We further show that the PPIase activity is important for the function of CYP71 in miRNA production. Our findings reveal orchestration of miRNA processing by a cyclophilin protein and suggest the involvement of peptidyl-prolyl cis-trans isomerization, a structural mechanism, in SE phase separation and miRNA processing.
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Affiliation(s)
- Gaozhan Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Jinrong Niu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Zhuoyan Hai
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Tengfei Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Dongqi Xie
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
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4
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Wieczorek P, Jarmołowski A, Szweykowska-Kulińska Z, Kozak M, Taube M. Solution structure and behaviour of the Arabidopsis thaliana HYL1 protein. Biochim Biophys Acta Gen Subj 2023; 1867:130376. [PMID: 37150226 DOI: 10.1016/j.bbagen.2023.130376] [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] [Received: 01/30/2023] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
In plants, microRNA biogenesis involves the complex assembly of molecular processes that are mostly governed by three proteins: RNase III protein DCL1 and two RNA binding proteins, SERRATE and HYL1. HYL1 protein is a double stranded RNA binding protein that is needed for the precise excision of miRNA/miRNA* duplex from the stem-loop containing primary miRNA gene transcripts. Moreover, HYL1 protein partners with HSP90 and CARP9 proteins to load the miRNA molecules onto the AGO1 endonuclease. HYL1 protein as a crucial player in the biogenesis pathway is regulated by its phosphorylation status to fine tune the levels of miRNA in various physiological conditions. HYL1 protein consists of two dsRNA binding domains (dsRBD) that are involved in RNA binding and dimerization and a C-terminal disordered tail of unknown function. Although the spatial structures of the individual dsRBDs have been determined there is a lack of information about the behaviour and structure of the full length protein. Using small the angle X-ray scattering (SAXS) technique we investigated the structure and dynamic of the HYL1 protein from Arabidopsis thaliana in solution. We show that the C-terminal domain is disordered and dynamic in solution and that HYL1 protein dimerization is dependent on the concentration. HYL1 protein lacking a C-terminal tail and a nuclear localisation signal (NLS) fragment is almost exclusively monomeric and similarly to full-length protein has a dynamic nature in solution. Our results point for the first time to the role of the C-terminal fragment in stabilisation of HYL1 dimer formation.
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Affiliation(s)
- Przemysław Wieczorek
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Michał Taube
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland.
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5
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Jozwiak M, Bielewicz D, Szweykowska-Kulinska Z, Jarmolowski A, Bajczyk M. SERRATE: a key factor in coordinated RNA processing in plants. TRENDS IN PLANT SCIENCE 2023; 28:841-853. [PMID: 37019716 DOI: 10.1016/j.tplants.2023.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 06/17/2023]
Abstract
The SERRATE (SE) protein is involved in the processing of RNA polymerase II (RNAPII) transcripts. It is associated with different complexes engaged in different aspects of plant RNA metabolism, including assemblies involved in transcription, splicing, polyadenylation, miRNA biogenesis, and RNA degradation. SE stability and interactome properties can be influenced by phosphorylation. SE exhibits an intriguing liquid-liquid phase separation property that may be important in the assembly of different RNA-processing bodies. Therefore, we propose that SE seems to participate in the coordination of different RNA-processing steps and can direct the fate of transcripts, targeting them for processing or degradation when they cannot be properly processed or are synthesized in excess.
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Affiliation(s)
- Monika Jozwiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Dawid Bielewicz
- Center for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
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6
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Bielewicz D, Dolata J, Bajczyk M, Szewc L, Gulanicz T, Bhat SS, Karlik A, Jozwiak M, Jarmolowski A, Szweykowska-Kulinska Z. Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes. PLANT & CELL PHYSIOLOGY 2023; 64:571-582. [PMID: 37040378 DOI: 10.1093/pcp/pcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 06/16/2023]
Abstract
Hyponastic Leaves 1 (HYL1) [also known as Double-stranded RNA-Binding protein 1 (DRB1)] is a double-stranded RNA-binding protein involved in microRNA (miRNA) processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the Dicer-Like 1 protein. In this work, we report a novel function of the HYL1 protein in the transcription of miRNA (MIR) genes. HYL1 colocalizes with RNA polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that the HYL1 protein interacts with many transcription factors. Finally, we show that the action of HYL1 is not limited to MIR genes and impacts the expression of many other genes, a majority of which are involved in plastid organization. These discoveries indicate HYL1 as an additional player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.
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Affiliation(s)
- Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Advanced Technologies, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun 87-100, Poland
| | - Susheel S Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Anna Karlik
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Monika Jozwiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
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7
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Musallam A, Abu-Romman S, Sadder MT. Molecular Characterization of Dehydrin in Azraq Saltbush among Related Atriplex Species. BIOTECH 2023; 12:biotech12020027. [PMID: 37092471 PMCID: PMC10123722 DOI: 10.3390/biotech12020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/25/2023] Open
Abstract
Atriplex spp. (saltbush) is known to survive extremely harsh environmental stresses such as salinity and drought. It mitigates such conditions based on specialized physiological and biochemical characteristics. Dehydrin genes (DHNs) are considered major players in this adaptation. In this study, a novel DHN gene from Azrak (Jordan) saltbush was characterized along with other Atriplex species from diverse habitats. Intronless DHN-expressed sequence tags (495-761 bp) were successfully cloned and sequenced. Saltbush dehydrins contain one S-segment followed by three K-segments: an arrangement called SK3-type. Two substantial insertions were detected including three copies of the K2-segemnet in A. canescens. New motif variants other than the six-serine standard were evident in the S-segment. AhaDHN1 (A. halimus) has a cysteine residue (SSCSSS), while AgaDHN1 (A. gardneri var. utahensis) has an isoleucine residue (SISSSS). In contrast to the conserved K1-segment, both the K2- and K3-segment showed several substitutions, particularly in AnuDHN1 (A. nummularia). In addition, a parsimony phylogenetic tree based on homologs from related genera was constructed. The phylogenetic tree resolved DHNs for all of the investigated Atriplex species in a superclade with an 85% bootstrap value. Nonetheless, the DHN isolated from Azraq saltbush was uniquely subclustred with a related genera Halimione portulacoides. The characterized DHNs revealed tremendous diversification among the Atriplex species, which opens a new venue for their functional analysis.
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Affiliation(s)
- Anas Musallam
- Biotechnology Research Directorate, National Agricultural Research Center, Baq'a 19381, Jordan
| | - Saeid Abu-Romman
- Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa Applied University, Al-Salt 19117, Jordan
| | - Monther T Sadder
- Plant Biotechnology Lab, Department of Horticulture and Crop Science, School of Agriculture, University of Jordan, Amman 11942, Jordan
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8
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Chen W, Zhu T, Shi Y, Chen Y, Li WJ, Chan RJ, Chen D, Zhang W, Yuan YA, Wang X, Sun B. An antisense intragenic lncRNA SEAIRa mediates transcriptional and epigenetic repression of SERRATE in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2216062120. [PMID: 36857348 PMCID: PMC10013867 DOI: 10.1073/pnas.2216062120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/27/2023] [Indexed: 03/02/2023] Open
Abstract
SERRATE (SE) is a core protein for microRNA (miRNA) biogenesis as well as for mRNA alternative splicing. Investigating the regulatory mechanism of SE expression is hence critical to understanding its detailed function in diverse biological processes. However, little about the control of SE expression has been clarified, especially through long noncoding RNA (lncRNA). Here, we identified an antisense intragenic lncRNA transcribed from the 3' end of SE, named SEAIRa. SEAIRa repressed SE expression, which in turn led to serrated leaves. SEAIRa recruited plant U-box proteins PUB25/26 with unreported RNA binding ability and a ubiquitin-like protein related to ubiquitin 1 (RUB1) for H2A monoubiquitination (H2Aub) at exon 11 of SE. In addition, PUB25/26 helped cleave SEAIRa and release the 5' domain fragment, which recruited the PRC2 complex for H3 lysine 27 trimethylation (H3K27me3) deposition at the first exon of SE. The distinct modifications of H2Aub and H3K27me3 at different sites of the SE locus cooperatively suppressed SE expression. Collectively, our results uncover an epigenetic mechanism mediated by the lncRNA SEAIRa that modulates SE expression, which is indispensable for plant growth and development.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210023, China
- Department of Biological Sciences, National University of Singapore, Singapore117543, Singapore
- Centre for BioImaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210023, China
| | - Yining Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing, Jiangsu210095, China
| | - Ying Chen
- Department of Biological Sciences, National University of Singapore, Singapore117543, Singapore
- Centre for BioImaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Wei Jian Li
- Department of Biological Sciences, National University of Singapore, Singapore117543, Singapore
- Centre for BioImaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Ru Jing Chan
- Department of Biological Sciences, National University of Singapore, Singapore117543, Singapore
- Centre for BioImaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210023, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing, Jiangsu210095, China
| | - Yuren Adam Yuan
- Department of Biological Sciences, National University of Singapore, Singapore117543, Singapore
- Centre for BioImaging Sciences, National University of Singapore, Singapore117557, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore117604, Singapore
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing, Jiangsu210095, China
| | - Bo Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210023, China
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9
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Stepien A, Dolata J, Gulanicz T, Bielewicz D, Bajczyk M, Smolinski DJ, Szweykowska-Kulinska Z, Jarmolowski A. Chromatin-associated microprocessor assembly is regulated by the U1 snRNP auxiliary protein PRP40. THE PLANT CELL 2022; 34:4920-4935. [PMID: 36087009 PMCID: PMC9709975 DOI: 10.1093/plcell/koac278] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/05/2022] [Indexed: 06/01/2023]
Abstract
In plants, microRNA (miRNA) biogenesis involves cotranscriptional processing of RNA polymerase II (RNAPII)-generated primary transcripts by a multi-protein complex termed the microprocessor. Here, we report that Arabidopsis (Arabidopsis thaliana) PRE-MRNA PROCESSING PROTEIN 40 (PRP40), the U1 snRNP auxiliary protein, positively regulates the recruitment of SERRATE, a core component of the plant microprocessor, to miRNA genes. The association of DICER-LIKE1 (DCL1), the microprocessor endoribonuclease, with chromatin was altered in prp40ab mutant plants. Impaired cotranscriptional microprocessor assembly was accompanied by RNAPII accumulation at miRNA genes and retention of miRNA precursors at their transcription sites in the prp40ab mutant plants. We show that cotranscriptional microprocessor assembly, regulated by AtPRP40, positively affects RNAPII transcription of miRNA genes and is important to reach the correct levels of produced miRNAs.
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Affiliation(s)
| | | | | | | | - Mateusz Bajczyk
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Dariusz J Smolinski
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun 87-100, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun 87-100, Poland
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10
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Affiliation(s)
- Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Department of Biology, Texas A&M University, College Station, TX, USA.
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11
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Gonzalo L, Tossolini I, Gulanicz T, Cambiagno DA, Kasprowicz-Maluski A, Smolinski DJ, Mammarella MF, Ariel FD, Marquardt S, Szweykowska-Kulinska Z, Jarmolowski A, Manavella PA. R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants. NATURE PLANTS 2022; 8:402-418. [PMID: 35449404 PMCID: PMC9023350 DOI: 10.1038/s41477-022-01125-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/08/2022] [Indexed: 05/03/2023]
Abstract
In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.
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Affiliation(s)
- Lucia Gonzalo
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ileana Tossolini
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - 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, Santa Fe, Argentina
- Unidad de Estudios Agropecuarios (UDEA), INTA-CONICET, Córdoba, Argentina
| | - Anna Kasprowicz-Maluski
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Dariusz Jan Smolinski
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - María Florencia Mammarella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, 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, Santa Fe, Argentina
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
| | - 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, Santa Fe, Argentina.
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12
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Wang L, Yan X, Li Y, Wang Z, Chhajed S, Shang B, Wang Z, Choi SW, Zhao H, Chen S, Zhang X. PRP4KA phosphorylates SERRATE for degradation via 20 S proteasome to fine-tune miRNA production in Arabidopsis. SCIENCE ADVANCES 2022; 8:eabm8435. [PMID: 35333566 PMCID: PMC8956257 DOI: 10.1126/sciadv.abm8435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phosphorylation can quickly switch on/off protein functions. Here, we reported pre-mRNA processing 4 kinase A (PRP4KA), and its paralogs interact with Serrate (SE), a key factor in RNA processing. PRP4KA phosphorylates at least five residues of SE in vitro and in vivo. Hypophosphorylated, but not hyperphosphorylated, SE variants could readily rescue se phenotypes in vivo. Moreover, hypophosphorylated SE variants had stronger binding affinity to microprocessor component HYL1 and were more resistant to degradation by 20S proteasome than hyperphosphorylated counterparts. Knockdown of the kinases enhanced the accumulation of hypophosphorylated SE. However, the excessive SE interfered with the assembly and function of SE-scaffolded macromolecule complexes, causing the se-like defects in the mutant and wild-type backgrounds. Thus, phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates miRNA metabolism through controlling homeostasis of SE accumulation in plants.
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Affiliation(s)
- Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shweta Chhajed
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Suk Won Choi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hongwei Zhao
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Sixue Chen
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Corresponding author.
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13
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Zhang L, Xiang Y, Chen S, Shi M, Jiang X, He Z, Gao S. Mechanisms of MicroRNA Biogenesis and Stability Control in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:844149. [PMID: 35350301 PMCID: PMC8957957 DOI: 10.3389/fpls.2022.844149] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, non-coding RNAs, which is 20-24 nucleotide long, regulate the expression of its target genes post-transcriptionally and play critical roles in plant normal growth, development, and biotic and abiotic stresses. In cells, miRNA biogenesis and stability control are important in regulating intracellular miRNA abundance. In addition, research on these two aspects has achieved fruitful results. In this review, we focus on the recent research progress in our understanding of miRNA biogenesis and their stability control in plants.
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Affiliation(s)
- Lu Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yu Xiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shengbo Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Min Shi
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xianda Jiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Zhuoli He
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shuai Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
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14
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Lange H, Gagliardi D. Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes. THE PLANT CELL 2022; 34:967-988. [PMID: 34954803 PMCID: PMC8894942 DOI: 10.1093/plcell/koab310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 05/08/2023]
Abstract
RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.
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Affiliation(s)
- Heike Lange
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Author for correspondence:
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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15
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Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021; 12:652189. [PMID: 34249082 PMCID: PMC8264776 DOI: 10.3389/fgene.2021.652189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
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Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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16
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ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control. Biochem Soc Trans 2021; 49:1325-1336. [PMID: 34060620 DOI: 10.1042/bst20201008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/26/2023]
Abstract
ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.
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17
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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18
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Mou M, Wang Q, Chen Y, Yu D, Chen L. Functional characterization of the Arabidopsis SERRATE under salt stress. PLANT DIVERSITY 2021; 43:71-77. [PMID: 33778227 PMCID: PMC7987573 DOI: 10.1016/j.pld.2020.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 06/12/2023]
Abstract
SERRATE (SE) plays critical roles in RNA metabolism and plant growth regulation. However, its function in stress-response processes remains largely unknown. Here, we examined the regulatory role of SE using the se-1 mutant and its complementation line under saline conditions. The expression of SE was repressed by salt treatment at both mRNA and protein levels. After treatment with different NaCl concentrations, the se-1 mutants showed increased sensitivity to salinity. This heightened sensitivity was evidenced by decreased germination, reduced root growth, more serious chlorosis, and increased conductivity of the mutants compared with the wild type. Further analysis revealed that SE regulates the pre-mRNA splicing of several well-characterized marker genes associated with salt stress tolerance. Our data thus imply that SE may function as a key component in plant response to salt stress by modulating the splicing of salt stress-associated genes.
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Affiliation(s)
- Minghui Mou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qijuan Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanli Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Ligang Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
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19
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Xie D, Chen M, Niu J, Wang L, Li Y, Fang X, Li P, Qi Y. Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis. Nat Cell Biol 2021; 23:32-39. [PMID: 33288888 DOI: 10.1038/s41556-020-00606-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/26/2020] [Indexed: 01/28/2023]
Abstract
MicroRNA (miRNA) production entails the step-wise processing of primary miRNAs (pri-miRNAs) into precursor miRNAs (pre-miRNAs) and miRNA/* duplexes by Dicing complexes containing DCL1, HYL1 and SE, which are localized in nuclear dicing bodies (D-bodies)1,2. Here, we show that D-bodies are phase-separated condensates. SE forms droplets and drives DCL1, HYL1 and pri/pre-miRNAs into the droplets in vitro, and mutation of SE abrogates the formation of D-bodies in vivo, which indicates that D-bodies arise through SE-mediated phase separation. Disruption of SE phase separation greatly reduces its activity in promoting miRNA processing both in vitro and in vivo. We further show that pre-miRNAs are processed into miRNA/* duplexes in the droplets and, after processing, miRNA/* duplexes are bound by HYL1 and released from the droplets. Our findings provide evidence that efficient miRNA processing depends on the SE-phase-separation-mediated formation of D-bodies and suggest a paradigm that the products made in phase-separated condensates can be shipped out for subsequent processes.
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Affiliation(s)
- Dongqi Xie
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jinrong Niu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Liang Wang
- Tsinghua-Peking Center for Life Sciences, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pilong Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, China. .,Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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20
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Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021. [PMID: 34249082 DOI: 10.1101/2020.04.29.068379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
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Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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21
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Bajczyk M, Lange H, Bielewicz D, Szewc L, Bhat SS, Dolata J, Kuhn L, Szweykowska-Kulinska Z, Gagliardi D, Jarmolowski A. SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis. Nucleic Acids Res 2020; 48:6839-6854. [PMID: 32449937 PMCID: PMC7337926 DOI: 10.1093/nar/gkaa373] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.
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Affiliation(s)
- Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Heike Lange
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Susheel S Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
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22
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MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities. Proc Natl Acad Sci U S A 2020; 117:23982-23990. [PMID: 32887800 DOI: 10.1073/pnas.2008283117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels in mac5 is partially caused by XRN2/XRN3, the nuclear-localized 5'-to-3' exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.
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23
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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 PHYSIOLOGY 2020; 184:316-329. [PMID: 32636339 PMCID: PMC7479909 DOI: 10.1104/pp.20.00258] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [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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24
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Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Maček B, Balasubramanian S, Bayer M, Jürgens G. The integral spliceosomal component CWC15 is required for development in Arabidopsis. Sci Rep 2020; 10:13336. [PMID: 32770129 PMCID: PMC7415139 DOI: 10.1038/s41598-020-70324-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Cameron H Lee
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Martina Kolb
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Craig Dent
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Yingjing Miao
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Steffen Lau
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | | | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany.
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25
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Li Y, Sun D, Ma Z, Yamaguchi K, Wang L, Zhong S, Yan X, Shang B, Nagashima Y, Koiwa H, Han J, Xie Q, Zhou M, Wang Z, Zhang X. Degradation of SERRATE via ubiquitin-independent 20S proteasome to survey RNA metabolism. NATURE PLANTS 2020; 6:970-982. [PMID: 32690892 PMCID: PMC7426255 DOI: 10.1038/s41477-020-0721-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/16/2020] [Indexed: 05/18/2023]
Abstract
SERRATE (SE) is a key factor in RNA metabolism. Here, we report that SE binds 20S core proteasome α subunit G1 (PAG1) among other components and is accumulated in their mutants. Purified PAG1-containing 20S proteasome degrades recombinant SE via an ATP- and ubiquitin-independent manner in vitro. Nevertheless, PAG1 is a positive regulator for SE in vivo, as pag1 shows comparable molecular and/or developmental defects relative to se. Furthermore, SE is poorly assembled into macromolecular complexes, exemplified by the microprocessor in pag1 compared with Col-0. SE overexpression triggered the destruction of both transgenic and endogenous protein, leading to similar phenotypes of se and SE overexpression lines. We therefore propose that PAG1 degrades the intrinsically disordered portion of SE to secure the functionality of folded SE that is assembled and protected in macromolecular complexes. This study provides insight into how the 20S proteasome regulates RNA metabolism through controlling its key factor in eukaryotes.
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Affiliation(s)
- Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Karissa Yamaguchi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Yukihiro Nagashima
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Jiajia Han
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
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26
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Li X, Chen P, Xie Y, Yan Y, Wang L, Dang H, Zhang J, Xu L, Ma F, Guan Q. Apple SERRATE negatively mediates drought resistance by regulating MdMYB88 and MdMYB124 and microRNA biogenesis. HORTICULTURE RESEARCH 2020; 7:98. [PMID: 32637126 PMCID: PMC7326988 DOI: 10.1038/s41438-020-0320-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 05/14/2023]
Abstract
The function of serrate (SE) in miRNA biogenesis in Arabidopsis is well elucidated, whereas its role in plant drought resistance is largely unknown. In this study, we report that MdSE acts as a negative regulator of apple (Malus × domestica) drought resistance by regulating the expression levels of MdMYB88 and MdMYB124 and miRNAs, including mdm-miR156, mdm-miR166, mdm-miR172, mdm-miR319, and mdm-miR399. MdSE interacts with MdMYB88 and MdMYB124, two positive regulators of apple drought resistance. MdSE decreases the transcript and protein levels of MdMYB88 and MdMYB124, which directly regulate the expression of MdNCED3, a key enzyme in abscisic acid (ABA) biosynthesis. Furthermore, MdSE is enriched in the same region of the MdNECD3 promoter where MdMYB88/MdMYB124 binds. Consistently, MdSE RNAi transgenic plants are more sensitive to ABA-induced stomatal closure, whereas MdSE OE plants are less sensitive. In addition, under drought stress, MdSE is responsible for the biogenesis of mdm-miR399, a negative regulator of drought resistance, and negatively regulates miRNAs, including mdm-miR156, mdm-miR166, mdm-miR172, and mdm-miR319, which are positive regulators of drought resistance. Taken together, by revealing the negative role of MdSE, our results broaden our understanding of the apple drought response and provide a candidate gene for apple drought improvement through molecular breeding.
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Affiliation(s)
- Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Huan Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Lingfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR 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, 712100 Shaanxi PR China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
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27
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Hivert G, Davidovich-Rikanati R, Bar E, Sitrit Y, Schaffer A, Dudareva N, Lewinsohn E. Prenyltransferases catalyzing geranyldiphosphate formation in tomato fruit. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110504. [PMID: 32540020 DOI: 10.1016/j.plantsci.2020.110504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/11/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Monoterpenes contribute either favorably or adversely to the flavor of tomato, yet modern tomato varieties generally lack monoterpenes in their fruit. The main immediate biosynthetic precursor of monoterpenes is geranyldiphosphate (GPP), produced by the action of GPP synthases (GPPSs). Plant GPPSs are often heteromeric enzymes consisting of a non-catalytic small subunit (GPPS.SSU) and a large subunit (GPPS.LSU), the latter similar to geranylgeranyldiphosphate synthases (GGPPSs) which generate longer prenylphosphate chains. We show here that LeGGPPS2, an enzyme previously reported to support carotenoid biosynthesis, can synthesize farnesyldiphosphate (FPP) and GPP in vitro, in addition to geranylgeranyldiphosphate, depending on the assay conditions. Moreover, GPP formation is favored in vitro by the interaction of LeGGPPS2 with GPPS.SSU from either Anthirrhinum majus (AmGPPS.SSU) or from a newly discovered GPPS.SSU ortholog present in the genome of M82 tomato. SlGPPS.SSU is not expressed in M82 tomato fruit but its orthologs are expressed in fruit of wild tomato relatives, such as Solanum pimpinelifollium and S. cheesmaniae that accumulate monoterpenes.
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Affiliation(s)
- Gal Hivert
- Department of Vegetable Crops, Newe Ya'ar Research Center, Agricultural Research Organization, The Volcani Center, P.O. Box 1021, Ramat Yishay, 30095, Israel; Department of Vegetable Crops, The Robert Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100001 Israel
| | - Rachel Davidovich-Rikanati
- Department of Vegetable Crops, Newe Ya'ar Research Center, Agricultural Research Organization, The Volcani Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Einat Bar
- Department of Vegetable Crops, Newe Ya'ar Research Center, Agricultural Research Organization, The Volcani Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Yaron Sitrit
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Arthur Schaffer
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, P.O Box 6, Bet Dagan 50250, Israel
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-1165, USA
| | - Efraim Lewinsohn
- Department of Vegetable Crops, Newe Ya'ar Research Center, Agricultural Research Organization, The Volcani Center, P.O. Box 1021, Ramat Yishay, 30095, Israel; Department of Vegetable Crops, The Robert Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100001 Israel.
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28
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Yu Y, Andreu-Agullo C, Liu BF, Barboza L, Toth M, Lai EC. Regulation of embryonic and adult neurogenesis by Ars2. Development 2020; 147:147/2/dev180018. [PMID: 31969356 DOI: 10.1242/dev.180018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022]
Abstract
Neural development is controlled at multiple levels to orchestrate appropriate choices of cell fate and differentiation. Although more attention has been paid to the roles of neural-restricted factors, broadly expressed factors can have compelling impacts on tissue-specific development. Here, we describe in vivo conditional knockout analyses of murine Ars2, which has mostly been studied as a general RNA-processing factor in yeast and cultured cells. Ars2 protein expression is regulated during neural lineage progression, and is required for embryonic neural stem cell (NSC) proliferation. In addition, Ars2 null NSCs can still transition into post-mitotic neurons, but fail to undergo terminal differentiation. Similarly, adult-specific deletion of Ars2 compromises hippocampal neurogenesis and results in specific behavioral defects. To broaden evidence for Ars2 as a chromatin regulator in neural development, we generated Ars2 ChIP-seq data. Notably, Ars2 preferentially occupies DNA enhancers in NSCs, where it colocalizes broadly with NSC regulator SOX2. Ars2 association with chromatin is markedly reduced following NSC differentiation. Altogether, Ars2 is an essential neural regulator that interacts dynamically with DNA and controls neural lineage development.
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Affiliation(s)
- Yang Yu
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Celia Andreu-Agullo
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Bing Fang Liu
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Luendreo Barboza
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Miklos Toth
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
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29
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Wang J, Mei J, Ren G. Plant microRNAs: Biogenesis, Homeostasis, and Degradation. FRONTIERS IN PLANT SCIENCE 2019; 10:360. [PMID: 30972093 PMCID: PMC6445950 DOI: 10.3389/fpls.2019.00360] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/07/2019] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, tiny, non-coding RNAs, are master regulators of gene expression among most eukaryotes. Intracellular miRNA abundance is regulated under multiple levels of control including transcription, processing, RNA modification, RNA-induced silencing complex (RISC) assembly, miRNA-target interaction, and turnover. In this review, we summarize our current understanding of the molecular components and mechanisms that influence miRNA biogenesis, homeostasis, and degradation in plants. We also make comparisons with findings from other organisms where necessary.
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Affiliation(s)
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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