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Feng L, Yan W, Tang X, Wu H, Pan Y, Lu D, Ling-Hu Q, Liu Y, Liu Y, Song X, Ali M, Fang L, Guo H, Li B. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis. Commun Biol 2024; 7:474. [PMID: 38637717 PMCID: PMC11026412 DOI: 10.1038/s42003-024-06142-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants.
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Affiliation(s)
- Li Feng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Wei Yan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Xianli Tang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Huihui Wu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yajie Pan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Dongdong Lu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Qianyan Ling-Hu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yuelin Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Liang Fang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
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2
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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [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: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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3
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Tremblay BJM, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI. Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. Nat Commun 2024; 15:1724. [PMID: 38409232 PMCID: PMC10897432 DOI: 10.1038/s41467-024-46082-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
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Affiliation(s)
- Benjamin J M Tremblay
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Cristina P Santini
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yajiao Cheng
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Xue Zhang
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
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4
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Zakrzewska-Placzek M, Golisz-Mocydlarz A, Krzyszton M, Piotrowska J, Lichocka M, Kufel J. The nucleolar protein NOL12 is required for processing of large ribosomal subunit rRNA precursors in Arabidopsis. BMC PLANT BIOLOGY 2023; 23:538. [PMID: 37919659 PMCID: PMC10623804 DOI: 10.1186/s12870-023-04561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND NOL12 5'-3' exoribonucleases, conserved among eukaryotes, play important roles in pre-rRNA processing, ribosome assembly and export. The most well-described yeast counterpart, Rrp17, is required for maturation of 5.8 and 25S rRNAs, whereas human hNOL12 is crucial for the separation of the large (LSU) and small (SSU) ribosome subunit rRNA precursors. RESULTS In this study we demonstrate that plant AtNOL12 is also involved in rRNA biogenesis, specifically in the processing of the LSU rRNA precursor, 27S pre-rRNA. Importantly, the absence of AtNOL12 alters the expression of many ribosomal protein and ribosome biogenesis genes. These changes could potentially exacerbate rRNA biogenesis defects, or, conversely, they might stem from the disturbed ribosome assembly caused by delayed pre-rRNA processing. Moreover, exposure of the nol12 mutant to stress factors, including heat and pathogen Pseudomonas syringae, enhances the observed molecular phenotypes, linking pre-rRNA processing to stress response pathways. The aberrant rRNA processing, dependent on AtNOL12, could impact ribosome function, as suggested by improved mutant resistance to ribosome-targeting antibiotics. CONCLUSION Despite extensive studies, the pre-rRNA processing pathway in plants remains insufficiently characterized. Our investigation reveals the involvement of AtNOL12 in the maturation of rRNA precursors, correlating this process to stress response in Arabidopsis. These findings contribute to a more comprehensive understanding of plant ribosome biogenesis.
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Affiliation(s)
- Monika Zakrzewska-Placzek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, 02-106, Poland.
| | - Anna Golisz-Mocydlarz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Justyna Piotrowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, 02-106, Poland.
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5
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Alomari DZ, Schierenbeck M, Alqudah AM, Alqahtani MD, Wagner S, Rolletschek H, Borisjuk L, Röder MS. Wheat Grains as a Sustainable Source of Protein for Health. Nutrients 2023; 15:4398. [PMID: 37892473 PMCID: PMC10609835 DOI: 10.3390/nu15204398] [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: 09/10/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Protein deficiency is recognized among the major global health issues with an underestimation of its importance. Genetic biofortification is a cost-effective and sustainable strategy to overcome global protein malnutrition. This study was designed to focus on protein-dense grains of wheat (Triticum aestivum L.) and identify the genes governing grain protein content (GPC) that improve end-use quality and in turn human health. Genome-wide association was applied using the 90k iSELECT Infinium and 35k Affymetrix arrays with GPC quantified by using a proteomic-based technique in 369 wheat genotypes over three field-year trials. The results showed significant natural variation among bread wheat genotypes that led to detecting 54 significant quantitative trait nucleotides (QTNs) surpassing the false discovery rate (FDR) threshold. These QTNs showed contrasting effects on GPC ranging from -0.50 to +0.54% that can be used for protein content improvement. Further bioinformatics analyses reported that these QTNs are genomically linked with 35 candidate genes showing high expression during grain development. The putative candidate genes have functions in the binding, remobilization, or transport of protein. For instance, the promising QTN AX-94727470 on chromosome 6B increases GPC by +0.47% and is physically located inside the gene TraesCS6B02G384500 annotated as Trehalose 6-phosphate phosphatase (T6P), which can be employed to improve grain protein quality. Our findings are valuable for the enhancement of protein content and end-use quality in one of the major daily food resources that ultimately improve human nutrition.
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Affiliation(s)
- Dalia Z. Alomari
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Matías Schierenbeck
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
- CONICET CCT La Plata, La Plata 1900, Buenos Aires, Argentina
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Mashael Daghash Alqahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Steffen Wagner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Hardy Rolletschek
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Ljudmilla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
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Yuan Y, Mao X, Abubakar YS, Zheng W, Wang Z, Zhou J, Zheng H. Genome-Wide Characterization of the RNA Exosome Complex in Relation to Growth, Development, and Pathogenicity of Fusarium graminearum. Microbiol Spectr 2023; 11:e0505822. [PMID: 37158744 PMCID: PMC10269758 DOI: 10.1128/spectrum.05058-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
The RNA exosome complex is a conserved, multisubunit RNase complex that contributes to the processing and degradation of RNAs in mammalian cells. However, the roles of the RNA exosome in phytopathogenic fungi and how it relates to fungal development and pathogenicity remain unclear. Herein, we identified 12 components of the RNA exosome in the wheat fungal pathogen Fusarium graminearum. Live-cell imaging showed that all the components of the RNA exosome complex are localized in the nucleus. FgEXOSC1 and FgEXOSCA were successfully knocked out; they are both involved in the vegetative growth, sexual reproduction, and pathogenicity of F. graminearum. Moreover, deletion of FgEXOSC1 resulted in abnormal toxisomes, decreased deoxynivalenol (DON) production, and downregulation of the expression levels of DON biosynthesis genes. The RNA-binding domain and N-terminal region of FgExosc1 are required for its normal localization and functions. Transcriptome sequencing (RNA-seq) showed that the disruption of FgEXOSC1 resulted in differential expression of 3,439 genes. Genes involved in processing of noncoding RNA (ncRNA), rRNA and ncRNA metabolism, ribosome biogenesis, and ribonucleoprotein complex biogenesis were significantly upregulated. Furthermore, subcellular localization, green fluorescent protein (GFP) pulldown, and coimmunoprecipitation (co-IP) assays demonstrated that FgExosc1 associates with the other components of the RNA exosome to form the RNA exosome complex in F. graminearum. Deletion of FgEXOSC1 and FgEXOSCA reduced the relative expression of some of the other subunits of the RNA exosome. Deletion of FgEXOSC1 affected the localization of FgExosc4, FgExosc6, and FgExosc7. In summary, our study reveals that the RNA exosome is involved in vegetative growth, sexual reproduction, DON production, and pathogenicity of F. graminearum. IMPORTANCE The RNA exosome complex is the most versatile RNA degradation machinery in eukaryotes. However, little is known about how this complex regulates the development and pathogenicity of plant-pathogenic fungi. In this study, we systematically identified 12 components of the RNA exosome complex in Fusarium head blight fungus Fusarium graminearum and first unveiled their subcellular localizations and established their biological functions in relation to the fungal development and pathogenesis. All the RNA exosome components are localized in the nucleus. FgExosc1 and FgExoscA are both required for the vegetative growth, sexual reproduction, DON production and pathogenicity in F. graminearum. FgExosc1 is involved in ncRNA processing, rRNA and ncRNA metabolism process, ribosome biogenesis and ribonucleoprotein complex biogenesis. FgExosc1 associates with the other components of RNA exosome complex and form the exosome complex in F. graminearum. Our study provides new insights into the role of the RNA exosome in regulating RNA metabolism, which is associated with fungal development and pathogenicity.
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Affiliation(s)
- Yanping Yuan
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuzhao Mao
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakubu Saddeeq Abubakar
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Wenhui Zheng
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zonghua Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Zhou
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huawei Zheng
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
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7
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Wilson B, Su Z, Kumar P, Dutta A. XRN2 suppresses aberrant entry of tRNA trailers into argonaute in humans and Arabidopsis. PLoS Genet 2023; 19:e1010755. [PMID: 37146074 PMCID: PMC10191329 DOI: 10.1371/journal.pgen.1010755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/17/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a well-characterized class of small RNAs (sRNAs) that regulate gene expression post-transcriptionally. miRNAs function within a complex milieu of other sRNAs of similar size and abundance, with the best characterized being tRNA fragments or tRFs. The mechanism by which the RNA-induced silencing complex (RISC) selects for specific sRNAs over others is not entirely understood in human cells. Several highly expressed tRNA trailers (tRF-1s) are strikingly similar to microRNAs in length but are generally excluded from the microRNA effector pathway. This exclusion provides a paradigm for identifying mechanisms of RISC selectivity. Here, we show that 5' to 3' exoribonuclease XRN2 contributes to human RISC selectivity. Although highly abundant, tRF-1s are highly unstable and degraded by XRN2 which blocks tRF-1 accumulation in RISC. We also find that XRN mediated degradation of tRF-1s and subsequent exclusion from RISC is conserved in plants. Our findings reveal a conserved mechanism that prevents aberrant entry of a class of highly produced sRNAs into Ago2.
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Affiliation(s)
- Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Zhangli Su
- Department of Genetics, University of Alabama, Birmingham, Alabama, United States of America
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- Department of Genetics, University of Alabama, Birmingham, Alabama, United States of America
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8
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Hang R, Xu Y, Wang X, Hu H, Flynn N, You C, Chen X. Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation. Proc Natl Acad Sci U S A 2023; 120:e2301081120. [PMID: 37011204 PMCID: PMC10104536 DOI: 10.1073/pnas.2301081120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/07/2023] [Indexed: 04/05/2023] Open
Abstract
Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S ribosomal RNA (rRNA) 3' end maturation during late-stage 40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the genome-wide effects of eIF5B have not been studied at the single-nucleotide resolution in any organism, and 18S rRNA 3' end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3' end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3' end maturation or metabolism. We quantitatively defined processing hotspots and identified adenylation as the prevalent nontemplated RNA addition at the 3' ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNA interference to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3' portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions and were not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late 40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, messenger RNA (mRNA) translation initiation, and siRNA biogenesis in plants.
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Affiliation(s)
- Runlai Hang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Xufeng Wang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Hao Hu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Nora Flynn
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Chenjiang You
- College of Life Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong510642, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing100871, China
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9
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Ding N, Zhang B. microRNA production in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1096772. [PMID: 36743500 PMCID: PMC9893293 DOI: 10.3389/fpls.2023.1096772] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
In plants, microRNAs (miRNAs) associate with ARGONAUTE (AGO) proteins and act as sequence-specific repressors of target gene expression, at the post-transcriptional level through target transcript cleavage and/or translational inhibition. MiRNAs are mainly transcribed by DNA-dependent RNA polymerase II (POL II) and processed by DICER LIKE1 (DCL1) complex into 21∼22 nucleotide (nt) long. Although the main molecular framework of miRNA biogenesis and modes of action have been established, there are still new requirements continually emerging in the recent years. The studies on the involvement factors in miRNA biogenesis indicate that miRNA biogenesis is not accomplished separately step by step, but is closely linked and dynamically regulated with each other. In this article, we will summarize the current knowledge on miRNA biogenesis, including MIR gene transcription, primary miRNA (pri-miRNA) processing, miRNA AGO1 loading and nuclear export; and miRNA metabolism including methylation, uridylation and turnover. We will describe how miRNAs are produced and how the different steps are regulated. We hope to raise awareness that the linkage between different steps and the subcellular regulation are becoming important for the understanding of plant miRNA biogenesis and modes of action.
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10
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Wang Y, Sun Z, Wang L, Chen L, Ma L, Lv J, Qiao K, Fan S, Ma Q. GhBOP1 as a Key Factor of Ribosomal Biogenesis: Development of Wrinkled Leaves in Upland Cotton. Int J Mol Sci 2022; 23:ijms23179942. [PMID: 36077339 PMCID: PMC9456263 DOI: 10.3390/ijms23179942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Block of proliferation 1 (BOP1) is a key protein that helps in the maturation of ribosomes and promotes the progression of the cell cycle. However, its role in the leaf morphogenesis of cotton remains unknown. Herein, we report and study the function of GhBOP1 isolated from Gossypium hirsutum. The sequence alignment revealed that BOP1 protein was highly conserved among different species. The yeast two-hybrid experiments, bimolecular fluorescence complementation, and luciferase complementation techniques revealed that GhBOP1 interact with GhPES and GhWDR12. Subcellular localization experiments revealed that GhBOP1, GhPES and GhWDR12 were localized at the nucleolus. Suppression of GhBOP1 transcripts resulted in the uneven bending of leaf margins and the presence of young wrinkled leaves by virus-induced gene silencing assay. Abnormal palisade arrangements and the presence of large upper epidermal cells were observed in the paraffin sections of the wrinkled leaves. Meanwhile, a jasmonic acid-related gene, GhOPR3, expression was increased. In addition, a negative effect was exerted on the cell cycle and the downregulation of the auxin-related genes was also observed. These results suggest that GhBOP1 plays a critical role in the development of wrinkled cotton leaves, and the process is potentially modulated through phytohormone signaling.
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Affiliation(s)
- Yanwen Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
| | - Zhimao Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China
| | - Long Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
| | - Lingling Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
| | - Lina Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
| | - Jiaoyan Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
| | - Kaikai Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
- Hainan Yazhou Bay Seed Lab, Sanya 572000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572000, China
- Correspondence: (S.F.); (Q.M.)
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455099, China
- Correspondence: (S.F.); (Q.M.)
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11
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Thieffry A, López-Márquez D, Bornholdt J, Malekroudi MG, Bressendorff S, Barghetti A, Sandelin A, Brodersen P. PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave. THE PLANT CELL 2022; 34:2615-2637. [PMID: 35404429 PMCID: PMC9252474 DOI: 10.1093/plcell/koac108] [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: 02/03/2022] [Accepted: 04/07/2022] [Indexed: 05/13/2023]
Abstract
Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression. We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames in mRNA leader sequences. We also find that 60% of PAMP response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors (TFs) whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct mitogen-activated protein kinase control, support the notion that the rapidly induced TFs could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.
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Affiliation(s)
- Axel Thieffry
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Jette Bornholdt
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | | | - Simon Bressendorff
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Andrea Barghetti
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
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12
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Mutation of an Essential 60S Ribosome Assembly Factor MIDASIN 1 Induces Early Flowering in Arabidopsis. Int J Mol Sci 2022; 23:ijms23126509. [PMID: 35742952 PMCID: PMC9223865 DOI: 10.3390/ijms23126509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Ribosome biogenesis is tightly associated with plant growth and reproduction. Mutations in genes encoding ribosomal proteins (RPs) or ribosome biogenesis factors (RBFs) generally result in retarded growth and delayed flowering. However, the early-flowering phenotype resulting from the ribosome biogenesis defect is rarely reported. We previously identified that the AAA-ATPase MIDASIN 1 (MDN1) functions as a 60S RBF in Arabidopsis. Here, we found that its weak mutant mdn1-1 is early-flowering. Transcriptomic analysis showed that the expression of FLOWERING LOCUS C (FLC) is down-regulated, while that of some autonomous pathway genes and ABSCISIC ACID-INSENSITIVE 5 (ABI5) is up-regulated in mdn1-1. Phenotypic analysis revealed that the flowering time of mdn1-1 is severely delayed by increasing FLC expression, suggesting that the early flowering in mdn1-1 is likely associated with the downregulation of FLC. We also found that the photoperiod pathway downstream of CONSTANTS (CO) and FLOWERING LOCUS T (FT) might contribute to the early flowering in mdn1-1. Intriguingly, the abi5-4 allele completely blocks the early flowering in mdn1-1. Collectively, our results indicate that the ribosome biogenesis defect elicited by the mutation of MDN1 leads to early flowering by affecting multiple flowering regulation pathways.
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13
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Darriere T, Jobet E, Zavala D, Escande ML, Durut N, de Bures A, Blanco-Herrera F, Vidal EA, Rompais M, Carapito C, Gourbiere S, Sáez-Vásquez J. Upon heat stress processing of ribosomal RNA precursors into mature rRNAs is compromised after cleavage at primary P site in Arabidopsis thaliana. RNA Biol 2022; 19:719-734. [PMID: 35522061 PMCID: PMC9090299 DOI: 10.1080/15476286.2022.2071517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcription and processing of 45S rRNAs in the nucleolus are keystones of ribosome biogenesis. While these processes are severely impacted by stress conditions in multiple species, primarily upon heat exposure, we lack information about the molecular mechanisms allowing sessile organisms without a temperature-control system, like plants, to cope with such circumstances. We show that heat stress disturbs nucleolar structure, inhibits pre-rRNA processing and provokes imbalanced ribosome profiles in Arabidopsis thaliana plants. Notably, the accuracy of transcription initiation and cleavage at the primary P site in the 5’ETS (5’ External Transcribed Spacer) are not affected but the levels of primary 45S and 35S transcripts are, respectively, increased and reduced. In contrast, precursors of 18S, 5.8S and 25S RNAs are rapidly undetectable upon heat stress. Remarkably, nucleolar structure, pre-rRNAs from major ITS1 processing pathway and ribosome profiles are restored after returning to optimal conditions, shedding light on the extreme plasticity of nucleolar functions in plant cells. Further genetic and molecular analysis to identify molecular clues implicated in these nucleolar responses indicate that cleavage rate at P site and nucleolin protein expression can act as a checkpoint control towards a productive pre-rRNA processing pathway.
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Affiliation(s)
- T Darriere
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - E Jobet
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - D Zavala
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - M L Escande
- CNRS, Observatoire Océanologique de Banyuls s/ mer, Banyuls-sur-mer, France.,BioPIC Platform of the OOB, Banyuls-sur-mer, France
| | - N Durut
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - A de Bures
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - F Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Institute for Integrative Biology (IBio), Santiago, Chile
| | - E A Vidal
- Millennium Institute for Integrative Biology (IBio), Santiago, Chile.,Bioinformática, Facultad de Ciencias, Universidad MayorCentro de Genómica y , Santiago, Chile
| | - M Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS/Université de Strasbourg, Strasbourg, France
| | - C Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS/Université de Strasbourg, Strasbourg, France
| | - S Gourbiere
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - J Sáez-Vásquez
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
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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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Vigh ML, Bressendorff S, Thieffry A, Arribas-Hernández L, Brodersen P. Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis. Nucleic Acids Res 2022; 50:1396-1415. [PMID: 35037064 PMCID: PMC8860578 DOI: 10.1093/nar/gkab1289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5′-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.
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Affiliation(s)
- Maria L Vigh
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simon Bressendorff
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Axel Thieffry
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Brodersen
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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16
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Shanmugam T, Streit D, Schroll F, Kovacevic J, Schleiff E. Dynamics and thermal sensitivity of ribosomal RNA maturation paths in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab434. [PMID: 34591082 DOI: 10.1093/jxb/erab434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 06/13/2023]
Abstract
Ribosome biogenesis is a constitutive fundamental process for cellular function. Its rate of production depends on the rate of maturation of precursor ribosomal RNA (pre-rRNA). The rRNA maturation paths are marked by four dominant rate-limiting intermediates with cell-type variation of the processivity rate. We have identified that high temperature stress in plants, while halting the existing pre-rRNA maturation schemes, also transiently triggers an atypical pathway for 35S pre-rRNA processing. This pathway leads to production of an aberrant precursor rRNA, reminiscent of yeast 24S, encompassing 18S and 5.8S rRNA that do not normally co-occur together at sub-unit levels; this response is elicited specifically by high and not low temperatures. We show this response to be conserved in two other model crop plant species (Rice and Tomato). This pathway persists even after returning to normal growth conditions for 1 hour and is reset between 1-6 hours after stress treatment, likely, due to resumption of normal 35S pre-rRNA synthesis and processing. The heat-induced ITS2 cleavage-derived precursors and stalled P-A2-like precursors were heterogeneous in nature with a fraction containing polymeric (A) tails. Furthermore, high temperature treatment and subsequent fractionation resulted in polysome and precursor rRNA depletion.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Deniz Streit
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Schroll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Jelena Kovacevic
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
- Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
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17
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Wahba L, Hansen L, Fire AZ. An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans. Dev Cell 2021; 56:2295-2312.e6. [PMID: 34388368 PMCID: PMC8387450 DOI: 10.1016/j.devcel.2021.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and their ability to silence transcripts with imperfect complementarity have raised several (non-exclusive) models for the underlying drivers of sterility. Here, we report the extranuclear and transferable nature of the sterility driver, its suppression via mutations disrupting the endogenous RNAi and poly-uridylation machinery, and copy-number amplification at the ribosomal DNA locus. In piRNA-deficient animals, several small interfering RNA (siRNA) populations become increasingly overabundant in the generations preceding loss of germline function, including ribosomal siRNAs (risiRNAs). A concomitant increase in uridylated sense rRNA fragments suggests that poly-uridylation may potentiate RNAi-mediated gene silencing of rRNAs. We conclude that loss of the piRNA machinery allows for unchecked amplification of siRNA populations, originating from abundant highly structured RNAs, to deleterious levels.
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Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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18
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Maekawa S, Yanagisawa S. Ribosome biogenesis factor OLI2 and its interactor BRX1-2 are associated with morphogenesis and lifespan extension in Arabidopsis thaliana. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:117-125. [PMID: 34177331 PMCID: PMC8215454 DOI: 10.5511/plantbiotechnology.20.1224a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/24/2020] [Indexed: 06/13/2023]
Abstract
Mutations that reduce the expression of ribosomal proteins (RPs) or limit the activity of ribosome biogenesis-related factors frequently cause physiological and morphological changes in Arabidopsis. Arabidopsis OLI2/NOP2A, a homolog of yeast Nop2, encodes a nucleolar methyltransferase that is required for the maturation of the 25S ribosomal RNA of the 60S large ribosomal subunit. Mutant oli2 plants exhibit pointed leaves and shortened primary roots. In this study, detailed phenotypic analysis of oli2 mutant and OLI2 overexpressor lines revealed a range of phenotypes. Seeds produced by oli2 mutant and OLI2 overexpressor plants were lighter and heavier than wild-type seeds, respectively. Seeds of the oli2 mutant also showed delayed germination, whereas seeds from the OLI2 overexpressor lines germinated earlier than the wild type. The oli2 mutant also had fewer and shorter lateral roots than the wild type. The lateral root development phenotype in the oli2 mutant was similar to that of auxin-related mutants, but was not enhanced by exogenously supplied auxin. Furthermore, the oli2 mutant and OLI2 overexpressor lines were hypersensitive and less sensitive to high concentrations of sugar, respectively. Split-GFP-based bimolecular fluorescence complementation analysis revealed that OLI2 interacted with a nucleolar protein, BRX1-2, which is involved in rRNA processing for the large ribosomal subunit. Moreover, overexpression of OLI2 and BRX1-2 caused similar morphological changes, including extension of plant lifespans. These results suggest that the functions of OLI2 and its interactor BRX1-2 are intimately associated with a range of developmental events in Arabidopsis.
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Affiliation(s)
- Shugo Maekawa
- Biotechnology Research Center, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Shuichi Yanagisawa
- Biotechnology Research Center, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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19
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Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed ( Brassica napus L.). PLANTS 2021; 10:plants10030426. [PMID: 33668258 PMCID: PMC7996214 DOI: 10.3390/plants10030426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.
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20
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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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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Takagi M, Iwamoto N, Kubo Y, Morimoto T, Takagi H, Takahashi F, Nishiuchi T, Tanaka K, Taji T, Kaminaka H, Shinozaki K, Akimitsu K, Terauchi R, Shirasu K, Ichimura K. Arabidopsis SMN2/HEN2, Encoding DEAD-Box RNA Helicase, Governs Proper Expression of the Resistance Gene SMN1/RPS6 and Is Involved in Dwarf, Autoimmune Phenotypes of mekk1 and mpk4 Mutants. PLANT & CELL PHYSIOLOGY 2020; 61:1507-1516. [PMID: 32467981 DOI: 10.1093/pcp/pcaa071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
In Arabidopsis thaliana, a mitogen-activated protein kinase pathway, MEKK1-MKK1/MKK2-MPK4, is important for basal resistance and disruption of this pathway results in dwarf, autoimmune phenotypes. To elucidate the complex mechanisms activated by the disruption of this pathway, we have previously developed a mutant screening system based on a dwarf autoimmune line that overexpressed the N-terminal regulatory domain of MEKK1. Here, we report that the second group of mutants, smn2, had defects in the SMN2 gene, encoding a DEAD-box RNA helicase. SMN2 is identical to HEN2, whose function is vital for the nuclear RNA exosome because it provides non-ribosomal RNA specificity for RNA turnover, RNA quality control and RNA processing. Aberrant SMN1/RPS6 transcripts were detected in smn2 and hen2 mutants. Disease resistance against Pseudomonas syringae pv. tomato DC3000 (hopA1), which is conferred by SMN1/RPS6, was decreased in smn2 mutants, suggesting a functional connection between SMN1/RPS6 and SMN2/HEN2. We produced double mutants mekk1smn2 and mpk4smn2 to determine whether the smn2 mutations suppress the dwarf, autoimmune phenotypes of the mekk1 and mpk4 mutants, as the smn1 mutations do. As expected, the mekk1 and mpk4 phenotypes were suppressed by the smn2 mutations. These results suggested that SMN2 is involved in the proper function of SMN1/RPS6. The Gene Ontology enrichment analysis using RNA-seq data showed that defense genes were downregulated in smn2, suggesting a positive contribution of SMN2 to the genome-wide expression of defense genes. In conclusion, this study provides novel insight into plant immunity via SMN2/HEN2, an essential component of the nuclear RNA exosome.
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Affiliation(s)
- Momoko Takagi
- Faculty and Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
- United Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566 Japan
- Faculty of Agriculture, Tottori University, 4-101 Koyama Minami, Tottori, 680-8553 Japan
| | - Naoki Iwamoto
- Faculty and Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
| | - Yuta Kubo
- Faculty and Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
| | - Takayuki Morimoto
- Faculty and Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
| | - Hiroki Takagi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003 Japan
- Department of Bioproduction Science, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836 Japan
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan
| | - Takumi Nishiuchi
- Institute for Gene Research, Advanced Science Research Center, Kanazawa University, Takaramachi, Kanazawa, Ishikawa, 920-8640 Japan
| | - Keisuke Tanaka
- Nodai Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Hironori Kaminaka
- Faculty of Agriculture, Tottori University, 4-101 Koyama Minami, Tottori, 680-8553 Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan
| | - Kazuya Akimitsu
- Faculty and Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
- United Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566 Japan
| | - Ryohei Terauchi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003 Japan
- Laboratory of Crop Evolution, Graduate School of Agricultural Sciences, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuya Ichimura
- Faculty and Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
- United Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566 Japan
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23
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Abstract
Biogenesis of plant microRNAs (miRNAs) takes place in nuclear dicing bodies (D-bodies), where the ribonulease III-type enzyme Dicer-like 1 (DCL1) processes primary transcripts of miRNAs (pri-miRNAs) into miRNA/miRNA* (*, passenger strand) duplexes from either base-to-loop or loop-to-base directions. Hyponastic Leaves 1 (HYL1), a double-stranded RNA-binding protein, is crucial for efficient and accurate processing. However, whether HYL1 has additional function remains unknown. Here, we report that HYL1 plays a noncanonical role in protecting pri-miRNAs from nuclear exosome attack in addition to ensuring processing. Loss of functions in SOP1 or HEN2, two cofactors of the nucleoplasmic exosome, significantly suppressed the morphological phenotypes of hyl1-2 Remarkably, mature miRNAs generated from loop-to-base processing were partially but preferentially restored in the hyl1 sop1 and hyl1 hen2 double mutants. Accordingly, loop-to-base-processed pri-miRNAs accumulated to higher levels in double mutants. In addition, dysfunction of HEN2, but not of SOP1, in hyl1-2 resulted in overaccumulation of many base-to-loop-processed pri-miRNAs, with most of their respective miRNAs unaffected. In summary, our findings reveal an antagonistic action of exosome in pri-miRNA biogenesis and uncover dual roles of HYL1 in stabilizing and processing of pri-miRNAs.
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24
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Kopka J. Systematic Review of Plant Ribosome Heterogeneity and Specialization. FRONTIERS IN PLANT SCIENCE 2020; 11:948. [PMID: 32670337 PMCID: PMC7332886 DOI: 10.3389/fpls.2020.00948] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/10/2020] [Indexed: 05/25/2023]
Abstract
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Yin-Chen Hsieh
- Bioinformatics Subdivision, Wageningen University, Wageningen, Netherlands
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
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25
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Abstract
The RNA exosome is a ribonucleolytic multiprotein complex that is conserved and essential in all eukaryotes. Although we tend to speak of "the" exosome complex, it should be more correctly viewed as several different subtypes that share a common core. Subtypes of the exosome complex are present in the cytoplasm, the nucleus and the nucleolus of all eukaryotic cells, and carry out the 3'-5' processing and/or degradation of a wide range of RNA substrates.Because the substrate specificity of the exosome complex is determined by cofactors, the system is highly adaptable, and different organisms have adjusted the machinery to their specific needs. Here, we present an overview of exosome complexes and their cofactors that have been described in different eukaryotes.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany.
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26
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FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis. Nat Commun 2019; 10:4424. [PMID: 31562313 PMCID: PMC6765019 DOI: 10.1038/s41467-019-12379-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/06/2019] [Indexed: 01/29/2023] Open
Abstract
Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, it also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5'-3' RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5'-3' exonuclease genes XRN2 and XRN3, we find that a large number of 21-nt risiRNAs are generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlates with pre-rRNA processing defects in these mutants. We also show that these risiRNAs are loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.
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27
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Kobyłecki K, Drążkowska K, Kuliński TM, Dziembowski A, Tomecki R. Elimination of 01/A'-A0 pre-rRNA processing by-product in human cells involves cooperative action of two nuclear exosome-associated nucleases: RRP6 and DIS3. RNA (NEW YORK, N.Y.) 2018; 24:1677-1692. [PMID: 30266864 PMCID: PMC6239190 DOI: 10.1261/rna.066589.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/17/2018] [Indexed: 05/10/2023]
Abstract
Pre-rRNA processing generates mature 18S, 5.8S, and 28S/25S rRNAs through multistage removal of surrounding 5'-ETS/3'-ETS and intervening ITS1/ITS2 segments. Endonucleolytic activities release by-products, which need to be eliminated. Here, we investigated the interplay of exosome-associated 3'-5' exonucleases DIS3 and RRP6 in rRNA processing and by-product elimination in human cells. In agreement with previous reports, we observed accumulation of 5.8S and 18S precursors upon dysfunction of these enzymes. However, none of these phenotypes was so pronounced as previously overlooked accumulation of short RNA species derived from 5'-ETS (01/A'-A0), in cells with nonfunctional DIS3. We demonstrate that removal of 01/A'-A0 is independent of the XRN2 5'-3' exonucleolytic activity. Instead, it proceeds rapidly after A0 cleavage and occurs exclusively in the 3'-5' direction in several phases-following initiation by an unknown nuclease, the decay is executed by RRP6 with some contribution of DIS3, whereas the ultimate phase involves predominantly DIS3. Our data shed new light onto the role of human exosome in 5'-ETS removal. Furthermore, although 01/A'-A0 degradation involves the action of two nucleases associated with the exosome ring, similarly to 5.8S 3'-end maturation, it is likely that contrary to the latter process, RRP6 acts prior to or redundantly with DIS3.
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Affiliation(s)
- Kamil Kobyłecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Karolina Drążkowska
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz M Kuliński
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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28
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Singh SS, Naiyer S, Bharadwaj R, Kumar A, Singh YP, Ray AK, Subbarao N, Bhattacharya A, Bhattacharya S. Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis. J Biol Chem 2018; 293:16242-16260. [PMID: 30171071 DOI: 10.1074/jbc.ra118.004632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/10/2018] [Indexed: 01/24/2023] Open
Abstract
The 3'-5' exoribonuclease Rrp6 is a key enzyme in RNA homeostasis involved in processing and degradation of many stable RNA precursors, aberrant transcripts, and noncoding RNAs. We previously have shown that in the protozoan parasite Entamoeba histolytica, the 5'-external transcribed spacer fragment of pre-rRNA accumulates under serum starvation-induced growth stress. This fragment is a known target of degradation by Rrp6. Here, we computationally and biochemically characterized EhRrp6 and found that it contains the catalytically important EXO and HRDC domains and exhibits exoribonuclease activity with both unstructured and structured RNA substrates, which required the conserved DEDD-Y catalytic-site residues. It lacked the N-terminal PMC2NT domain for binding of the cofactor Rrp47, but could functionally complement the growth defect of a yeast rrp6 mutant. Of note, no Rrp47 homologue was detected in E. histolytica Immunolocalization studies revealed that EhRrp6 is present both in the nucleus and cytosol of normal E. histolytica cells. However, growth stress induced its complete loss from the nuclei, reversed by proteasome inhibitors. EhRrp6-depleted E. histolytica cells were severely growth restricted, and EhRrp6 overexpression protected the cells against stress, suggesting that EhRrp6 functions as a stress sensor. Importantly EhRrp6 depletion reduced erythrophagocytosis, an important virulence determinant of E. histolytica This reduction was due to a specific decrease in transcript levels of some phagocytosis-related genes (Ehcabp3 and Ehrho1), whereas expression of other genes (Ehcabp1, Ehcabp6, Ehc2pk, and Eharp2/3) was unaffected. This is the first report of the role of Rrp6 in cell growth and stress responses in a protozoan parasite.
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Affiliation(s)
| | | | - Ravi Bharadwaj
- the School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Amarjeet Kumar
- the School of Computational and Integrative Sciences, and
| | | | | | - Naidu Subbarao
- the School of Computational and Integrative Sciences, and
| | - Alok Bhattacharya
- the School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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29
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Singh P, Saha U, Paira S, Das B. Nuclear mRNA Surveillance Mechanisms: Function and Links to Human Disease. J Mol Biol 2018; 430:1993-2013. [PMID: 29758258 DOI: 10.1016/j.jmb.2018.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Production of export-competent mRNAs involves transcription and a series of dynamic processing and modification events of pre-messenger RNAs in the nucleus. Mutations in the genes encoding the transcription and mRNP processing machinery and the complexities involved in the biogenesis events lead to the formation of aberrant messages. These faulty transcripts are promptly eliminated by the nuclear RNA exosome and its cofactors to safeguard the cells and organisms from genetic catastrophe. Mutations in the components of the core nuclear exosome and its cofactors lead to the tissue-specific dysfunction of exosomal activities, which are linked to diverse human diseases and disorders. In this article, we examine the structure and function of both the yeast and human RNA exosome complex and its cofactors, discuss the nature of the various altered amino acid residues implicated in these diseases with the speculative mechanisms of the mutation-induced disorders and project the frontier and prospective avenues of the future research in this field.
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Affiliation(s)
- Pragyan Singh
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Upasana Saha
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India.
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30
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Wang H, Wang K, Du Q, Wang Y, Fu Z, Guo Z, Kang D, Li WX, Tang J. Maize Urb2 protein is required for kernel development and vegetative growth by affecting pre-ribosomal RNA processing. THE NEW PHYTOLOGIST 2018; 218:1233-1246. [PMID: 29479724 DOI: 10.1111/nph.15057] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Ribosome biogenesis is a fundamental process in eukaryotic cells. Although Urb2 protein has been implicated in ribosome biogenesis in yeast, the Urb2 domain is loosely conserved between plants and yeast, and the function of Urb2 protein in plants remains unknown. Here, we isolated a maize mutant, designated as urb2, with defects in kernel development and vegetative growth. Positional cloning and transgenic analysis revealed that urb2 encodes an Urb2 domain-containing protein. Compared with the wild-type (WT), the urb2 mutant showed decreased ratios of 60S/40S and 80S/40S and increased ratios of polyribosomes. The pre-rRNA intermediates of 35/33S rRNA, P-A3 and 18S-A3 were significantly accumulated in the urb2 mutant. Transcriptome profiling of the urb2 mutant indicated that ZmUrb2 affects the expression of a number of ribosome-related genes. We further demonstrated that natural variations in ZmUrb2 are significantly associated with maize kernel length. The overall results indicate that, by affecting pre-rRNA processing, the Urb2 protein is required for ribosome biogenesis in maize.
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Affiliation(s)
- Hongqiu Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Kai Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yafei Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dingming Kang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
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31
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Kojima K, Tamura J, Chiba H, Fukada K, Tsukaya H, Horiguchi G. Two Nucleolar Proteins, GDP1 and OLI2, Function As Ribosome Biogenesis Factors and Are Preferentially Involved in Promotion of Leaf Cell Proliferation without Strongly Affecting Leaf Adaxial-Abaxial Patterning in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 8:2240. [PMID: 29375609 PMCID: PMC5767255 DOI: 10.3389/fpls.2017.02240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/20/2017] [Indexed: 05/25/2023]
Abstract
Leaf abaxial-adaxial patterning is dependent on the mutual repression of leaf polarity genes expressed either adaxially or abaxially. In Arabidopsis thaliana, this process is strongly affected by mutations in ribosomal protein genes and in ribosome biogenesis genes in a sensitized genetic background, such as asymmetric leaves2 (as2). Most ribosome-related mutants by themselves do not show leaf abaxialization, and one of their typical phenotypes is the formation of pointed rather than rounded leaves. In this study, we characterized two ribosome-related mutants to understand how ribosome biogenesis is linked to several aspects of leaf development. Previously, we isolated oligocellula2 (oli2) which exhibits the pointed-leaf phenotype and has a cell proliferation defect. OLI2 encodes a homolog of Nop2 in Saccharomyces cerevisiae, a ribosome biogenesis factor involved in pre-60S subunit maturation. In this study, we found another pointed-leaf mutant that carries a mutation in a gene encoding an uncharacterized protein with a G-patch domain. Similar to oli2, this mutant, named g-patch domain protein1 (gdp1), has a reduced number of leaf cells. In addition, gdp1 oli2 double mutants showed a strong genetic interaction such that they synergistically impaired cell proliferation in leaves and produced markedly larger cells. On the other hand, they showed additive phenotypes when combined with several known ribosomal protein mutants. Furthermore, these mutants have a defect in pre-rRNA processing. GDP1 and OLI2 are strongly expressed in tissues with high cell proliferation activity, and GDP1-GFP and GFP-OLI2 are localized in the nucleolus. These results suggest that OLI2 and GDP1 are involved in ribosome biogenesis. We then examined the effects of gdp1 and oli2 on adaxial-abaxial patterning by crossing them with as2. Interestingly, neither gdp1 nor oli2 strongly enhanced the leaf polarity defect of as2. Similar results were obtained with as2 gdp1 oli2 triple mutants although they showed severe growth defects. These results suggest that the leaf abaxialization phenotype induced by ribosome-related mutations is not merely the result of a general growth defect and that there may be a sensitive process in the ribosome biogenesis pathway that affects adaxial-abaxial patterning when compromised by a mutation.
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Affiliation(s)
- Koji Kojima
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Junya Tamura
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Hiroto Chiba
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kanae Fukada
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Okazaki Institute for Integrative Bioscience, Okazaki, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
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32
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Liu Y, Imai R. Function of Plant DExD/H-Box RNA Helicases Associated with Ribosomal RNA Biogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:125. [PMID: 29472942 PMCID: PMC5809497 DOI: 10.3389/fpls.2018.00125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
Ribosome biogenesis is a highly complex process that requires several cofactors, including DExD/H-box RNA helicases (RHs). RHs are a family of ATPases that rearrange the secondary structures of RNA and thus remodel ribonucleoprotein complexes. DExD/H-box RHs are found in most organisms and play critical roles in a variety of RNA-involved cellular events. In human and yeast cells, many DExD/H box RHs participate in multiple steps of ribosome biogenesis and regulate cellular proliferation and stress responses. In plants, several DExD/H-box RHs have been demonstrated to be associated with plant development and abiotic stress tolerance through their functions in modulating pre-rRNA processing. In this review, we summarize the pleiotropic roles of DExD/H-box RHs in rRNA biogenesis and other biological functions. We also describe the overall function of the DExD/H-box RH family in ribosome biogenesis based on data from human and yeast.
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33
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Sikorska N, Zuber H, Gobert A, Lange H, Gagliardi D. RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities. Nat Commun 2017; 8:2162. [PMID: 29255150 PMCID: PMC5735172 DOI: 10.1038/s41467-017-02066-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
The RNA exosome provides eukaryotic cells with an essential 3'-5' exoribonucleolytic activity, which processes or eliminates many classes of RNAs. Its nine-subunit core (Exo9) is structurally related to prokaryotic phosphorolytic exoribonucleases. Yet, yeast and animal Exo9s have lost the primordial phosphorolytic capacity and rely instead on associated hydrolytic ribonucleases for catalytic activity. Here, we demonstrate that Arabidopsis Exo9 has retained a distributive phosphorolytic activity, which contributes to rRNA maturation processes, the hallmark of exosome function. High-density mapping of 3' extremities of rRNA maturation intermediates reveals the intricate interplay between three exoribonucleolytic activities coordinated by the plant exosome. Interestingly, the analysis of RRP41 protein diversity across eukaryotes suggests that Exo9's intrinsic activity operates throughout the green lineage, and possibly in some earlier-branching non-plant eukaryotes. Our results reveal a remarkable evolutionary variation of this essential RNA degradation machine in eukaryotes.
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Affiliation(s)
- Natalia Sikorska
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Hélène Zuber
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Anthony Gobert
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Heike Lange
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Dominique Gagliardi
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France.
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Shanmugam T, Abbasi N, Kim HS, Kim HB, Park NI, Park GT, Oh SA, Park SK, Muench DG, Choi Y, Park YI, Choi SB. An Arabidopsis divergent pumilio protein, APUM24, is essential for embryogenesis and required for faithful pre-rRNA processing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1092-1105. [PMID: 29031033 DOI: 10.1111/tpj.13745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 05/06/2023]
Abstract
Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization. Additionally, the mutant embryos displayed defects in cell patterning from pro-embryo through globular stages. The mutant embryos were marked by altered auxin maxima, which were substantiated by the mislocalization of PIN1 and PIN7 transporters in the defective embryos. Homozygous apum24 callus accumulates rRNA processing intermediates, including uridylated and adenylated 5.8S and 25S rRNA precursors. An RNA-protein interaction assay showed that the histidine-tagged recombinant APUM24 binds RNAin vitro with no apparent specificity. Overall, our results demonstrated that APUM24 is required for rRNA processing and early embryogenesis in Arabidopsis.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nazia Abbasi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Hyung-Sae Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Ho Bang Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nam-Il Park
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Guen Tae Park
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, South Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
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35
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Bassham DC, MacIntosh GC. Degradation of cytosolic ribosomes by autophagy-related pathways. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:169-174. [PMID: 28716412 DOI: 10.1016/j.plantsci.2017.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/08/2017] [Accepted: 05/13/2017] [Indexed: 05/08/2023]
Abstract
Ribosomes are essential molecular machines that require a large cellular investment, yet the mechanisms of their turnover are not well understood in any eukaryotic organism. Recent advances in Arabidopsis suggest that plants utilize selective mechanisms to transport rRNA or ribosomes to the vacuole, where rRNA is degraded and the breakdown products recycled to maintain cellular homeostasis. This review focuses on known mechanisms of rRNA turnover and explores unanswered questions on the specificity and pathways of ribosome turnover and the role of this process in maintenance of cellular homeostasis.
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Affiliation(s)
- Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
| | - Gustavo C MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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36
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Plötner B, Nurmi M, Fischer A, Watanabe M, Schneeberger K, Holm S, Vaid N, Schöttler MA, Walther D, Hoefgen R, Weigel D, Laitinen RAE. Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:251-262. [PMID: 28378460 DOI: 10.1111/tpj.13560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 05/28/2023]
Abstract
Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.
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Affiliation(s)
- Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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37
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Correction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:355-356. [PMID: 28670740 DOI: 10.1111/tpj.13594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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38
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Tomecki R, Sikorski PJ, Zakrzewska-Placzek M. Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases. FEBS Lett 2017; 591:1801-1850. [PMID: 28524231 DOI: 10.1002/1873-3468.12682] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/14/2017] [Accepted: 05/15/2017] [Indexed: 12/17/2022]
Abstract
Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
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Meola N, Jensen TH. Targeting the nuclear RNA exosome: Poly(A) binding proteins enter the stage. RNA Biol 2017; 14:820-826. [PMID: 28421898 DOI: 10.1080/15476286.2017.1312227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Centrally positioned in nuclear RNA metabolism, the exosome deals with virtually all transcript types. This 3'-5' exo- and endo-nucleolytic degradation machine is guided to its RNA targets by adaptor proteins that enable substrate recognition. Recently, the discovery of the 'Poly(A) tail exosome targeting (PAXT)' connection as an exosome adaptor to human nuclear polyadenylated transcripts has relighted the interest of poly(A) binding proteins (PABPs) in both RNA productive and destructive processes.
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Affiliation(s)
- Nicola Meola
- a Department of Molecular Biology and Genetics , Aarhus University , Aarhus C , Denmark
| | - Torben Heick Jensen
- a Department of Molecular Biology and Genetics , Aarhus University , Aarhus C , Denmark
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40
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Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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41
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Asha S, Soniya EV. The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages. Sci Rep 2017; 7:41052. [PMID: 28145468 PMCID: PMC5286533 DOI: 10.1038/srep41052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 12/16/2016] [Indexed: 01/27/2023] Open
Abstract
Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5.8S rRNA. The major cleavage process mapped identically among the different tissues of the same plant. The differential expression and cleavage of 5'5.8S srRNAs in Phytophthora capsici infected P. nigrum tissues indicated the critical biological functions of these srRNAs during stress response. The non-canonical short hairpin precursor structure, the association with Argonaute proteins, and the potential targets of 5'5.8S srRNAs reinforced their regulatory role in the RNAi pathway in plants. In addition, this novel lineage specific small RNAs may have tremendous biological potential in the taxonomic profiling of plants.
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Affiliation(s)
- Srinivasan Asha
- Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - E V Soniya
- Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
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42
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Patrick EM, Srinivasan S, Jankowsky E, Comstock MJ. The RNA helicase Mtr4p is a duplex-sensing translocase. Nat Chem Biol 2016; 13:99-104. [PMID: 27870836 DOI: 10.1038/nchembio.2234] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/29/2016] [Indexed: 12/30/2022]
Abstract
The conserved Saccharomyces cerevisiae Ski2-like RNA helicase Mtr4p plays essential roles in eukaryotic nuclear RNA processing. RNA helicase activity of Mtr4p is critical for biological functions of the enzyme, but the molecular basis for RNA unwinding is not understood. Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3'-to-5' translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps. We further show that RNA unwinding by Mtr4p requires interaction with upstream RNA duplex. Inclusion of Mtr4p within the TRAMP complex increases the rate constant for unwinding initiation but does not change the characteristics of Mtr4p's helicase mechanism. Our data indicate that Mtr4p utilizes a previously unknown unwinding mode that combines aspects of canonical translocating helicases and non-canonical duplex-sensing helicases, thereby restricting directional translocation to duplex regions.
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Affiliation(s)
- Eric M Patrick
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
| | - Sukanya Srinivasan
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western University, Cleveland, Ohio, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western University, Cleveland, Ohio, USA
| | - Matthew J Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
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Chen YJC, Wang HJ, Jauh GY. Dual Role of a SAS10/C1D Family Protein in Ribosomal RNA Gene Expression and Processing Is Essential for Reproduction in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006408. [PMID: 27792779 PMCID: PMC5085252 DOI: 10.1371/journal.pgen.1006408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022] Open
Abstract
In eukaryotic cells, ribosomal RNAs (rRNAs) are transcribed, processed, and assembled with ribosomal proteins in the nucleolus. Regulatory mechanisms of rRNA gene (rDNA) transcription and processing remain elusive in plants, especially their connection to nucleolar organization. We performed an in silico screen for essential genes of unknown function in Arabidopsis thaliana and identified Thallo (THAL) encoding a SAS10/C1D family protein. THAL disruption caused enlarged nucleoli in arrested embryos, aberrant processing of precursor rRNAs at the 5' External Transcribed Spacer, and repression of the major rDNA variant (VAR1). THAL overexpression lines showed de-repression of VAR1 and overall reversed effects on rRNA processing sites. Strikingly, THAL overexpression also induced formation of multiple nucleoli per nucleus phenotypic of mutants of heterochromatin factors. THAL physically associated with histone chaperone Nucleolin 1 (NUC1), histone-binding NUC2, and histone demethylase Jumonji 14 (JMJ14) in bimolecular fluorescence complementation assay, suggesting that it participates in chromatin regulation. Furthermore, investigation of truncated THAL proteins revealed that the SAS10 C-terminal domain is likely important for its function in chromatin configuration. THAL also interacted with putative Small Subunit processome components, including previously unreported Arabidopsis homologue of yeast M Phase Phosphoprotein 10 (MPP10). Our results uncovering the dual role of THAL in transcription and processing events critical for proper rRNA biogenesis and nucleolar organization during reproduction are the first to define the function of SAS10/C1D family members in plants.
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Affiliation(s)
- Ying-Jiun C. Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Huei-Jing Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taichung, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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45
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A Cold-Inducible DEAD-Box RNA Helicase from Arabidopsis thaliana Regulates Plant Growth and Development under Low Temperature. PLoS One 2016; 11:e0154040. [PMID: 27116354 PMCID: PMC4846089 DOI: 10.1371/journal.pone.0154040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 01/29/2023] Open
Abstract
DEAD-box RNA helicases comprise a large family and are involved in a range of RNA processing events. Here, we identified one of the Arabidopsis thaliana DEAD-box RNA helicases, AtRH7, as an interactor of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 (AtCSP3), which is an RNA chaperone involved in cold adaptation. Promoter:GUS transgenic plants revealed that AtRH7 is expressed ubiquitously and that its levels of the expression are higher in rapidly growing tissues. Knockout mutant lines displayed several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis. In addition, aberrant floral development was also observed in rh7 mutants. When the mutants were germinated at low temperature (12°C), both radicle and first leaf emergence were severely delayed; after exposure of seedlings to a long period of cold, the mutants developed aberrant, fewer, and smaller leaves. RNA blots and circular RT-PCR revealed that 35S and 18S rRNA precursors accumulated to higher levels in the mutants than in WT under both normal and cold conditions, suggesting the mutants are partially impaired in pre-rRNA processing. Taken together, the results suggest that AtRH7 affects rRNA biogenesis and plays an important role in plant growth under cold.
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Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier JA, Mockaitis K, Gagliardi D, Vaucheret H, Lange H, Faure JD. The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis. PLoS Genet 2016; 12:e1005817. [PMID: 26828932 PMCID: PMC4735120 DOI: 10.1371/journal.pgen.1005817] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
Correct gene expression requires tight RNA quality control both at transcriptional and post-transcriptional levels. Using a splicing-defective allele of PASTICCINO2 (PAS2), a gene essential for plant development, we isolated suppressor mutations modifying pas2-1 mRNA profiles and restoring wild-type growth. Three suppressor of pas2 (sop) mutations modified the degradation of mis-spliced pas2-1 mRNA species, allowing the synthesis of a functional protein. Cloning of the suppressor mutations identified the core subunit of the exosome SOP2/RRP4, the exosome nucleoplasmic cofactor SOP3/HEN2 and a novel zinc-finger protein SOP1 that colocalizes with HEN2 in nucleoplasmic foci. The three SOP proteins counteract post-transcriptional (trans)gene silencing (PTGS), which suggests that they all act in RNA quality control. In addition, sop1 mutants accumulate some, but not all of the misprocessed mRNAs and other types of RNAs that are observed in exosome mutants. Taken together, our data show that SOP1 is a new component of nuclear RNA surveillance that is required for the degradation of a specific subset of nuclear exosome targets.
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Affiliation(s)
- Kian Hématy
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- * E-mail:
| | - Yannick Bellec
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States of America
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Pauline Anne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Céline Morineau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Richard P. Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Frederic Beaudoin
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Johnathan A. Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Keithanne Mockaitis
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- Pervasive Technology Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Heike Lange
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Jean-Denis Faure
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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47
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Huang CK, Shen YL, Huang LF, Wu SJ, Yeh CH, Lu CA. The DEAD-Box RNA Helicase AtRH7/PRH75 Participates in Pre-rRNA Processing, Plant Development and Cold Tolerance in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:174-91. [PMID: 26637537 DOI: 10.1093/pcp/pcv188] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/18/2015] [Indexed: 05/18/2023]
Abstract
DEAD-box RNA helicases belong to an RNA helicase family that plays specific roles in various RNA metabolism processes, including ribosome biogenesis, mRNA splicing, RNA export, mRNA translation and RNA decay. This study investigated a DEAD-box RNA helicase, AtRH7/PRH75, in Arabidopsis. Expression of AtRH7/PRH75 was ubiquitous; however, the levels of mRNA accumulation were increased in cell division regions and were induced by cold stress. The phenotypes of two allelic AtRH7/PRH75-knockout mutants, atrh7-2 and atrh7-3, resembled auxin-related developmental defects that were exhibited in several ribosomal protein mutants, and were more severe under cold stress. Northern blot and circular reverse transcription-PCR (RT-PCR) analyses indicated that unprocessed 18S pre-rRNAs accumulated in the atrh7 mutants. The atrh7 mutants were hyposensitive to the antibiotic streptomycin, which targets ribosomal small subunits, suggesting that AtRH7 was also involved in ribosome assembly. In addition, the atrh7-2 and atrh7-3 mutants displayed cold hypersensitivity and decreased expression of CBF1, CBF2 and CBF3, which might be responsible for the cold intolerance. The present study indicated that AtRH7 participates in rRNA biogenesis and is also involved in plant development and cold tolerance in Arabidopsis.
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Affiliation(s)
- Chun-Kai Huang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC These authors contributed equally to this work
| | - Yu-Lien Shen
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC These authors contributed equally to this work
| | - Li-Fen Huang
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Shaw-Jye Wu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chin-Hui Yeh
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
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48
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Basbouss-Serhal I, Leymarie J, Bailly C. Fluctuation of Arabidopsis seed dormancy with relative humidity and temperature during dry storage. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:119-30. [PMID: 26428064 PMCID: PMC4682427 DOI: 10.1093/jxb/erv439] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The changes in germination potential of freshly harvested seeds of Arabidopsis thaliana stored in various combinations of temperature and relative humidity were investigated over 63 weeks of storage. Seeds of the wild type Col-0 and of two mutants displaying low and high levels of dormancy, cat2-1 and mtr4-1, respectively, were stored at harvest in 24 different environments including a combination of eight relative humidities, from 1 to 85%, and four temperatures (10, 15, 20, and 25 °C). These mutations did not influence behaviour of seeds during storage. Primary dormant seeds did not germinate in darkness at 25 °C but acquired the potential to germinate at this temperature within 7 weeks when stored in relative humidities close to 50% across all temperatures. Sorption isotherms and Arrhenius plots demonstrated that the seed moisture content of 0.06 g H2O/g dry weight was a critical value below which dormancy release was associated with reactions of negative activation energy and above which dormancy release increased with temperature. Longer storage times when relative humidity did not exceed 75-85% led to decreased germination at 25 °C, corresponding to the induction of secondary dormancy. Dormancy release and induction of secondary dormancy in the dry state were associated with induction or repression of key genes related to abscisic acid and gibberellins biosynthesis and signalling pathways. In high relative humidity, prolonged storage of seeds induced ageing and progressive loss of viability, but this was not related to the initial level of dormancy.
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Affiliation(s)
- Isabelle Basbouss-Serhal
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, 75005 Paris, France CNRS, UMR 7622, 75005 Paris, France
| | - Juliette Leymarie
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, 75005 Paris, France CNRS, UMR 7622, 75005 Paris, France
| | - Christophe Bailly
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, 75005 Paris, France CNRS, UMR 7622, 75005 Paris, France
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49
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Carlotto N, Wirth S, Furman N, Ferreyra Solari N, Ariel F, Crespi M, Kobayashi K. The chloroplastic DEVH-box RNA helicase INCREASED SIZE EXCLUSION LIMIT 2 involved in plasmodesmata regulation is required for group II intron splicing. PLANT, CELL & ENVIRONMENT 2016; 39:165-73. [PMID: 26147377 DOI: 10.1111/pce.12603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 05/18/2023]
Abstract
INCREASED SIZE EXCLUSION LIMIT 2 (ISE2) encodes a putative DEVH-box RNA helicase originally identified through a genetic screening for Arabidopsis mutants altered in plasmodesmata (PD) aperture. Depletion of ISE2 also affects chloroplasts activity, decreases accumulation of photosynthetic pigments and alters expression of photosynthetic genes. In this work, we show the chloroplast localization of ISE2 and decipher its role in plastidic RNA processing and, consequently, PD function. Group II intron-containing RNAs from chloroplasts exhibit defective splicing in ise2 mutants and ISE2-silenced plants, compromising plastid viability. Furthermore, RNA immunoprecipitation suggests that ISE2 binds in vivo to several splicing-regulated RNAs. Finally, we show that the chloroplast clpr2 mutant (defective in a subunit of a plastidic Clp protease) also exhibits abnormal PD function during embryogenesis, supporting the idea that chloroplast RNA processing is required to regulate cell-cell communication in plants.
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Affiliation(s)
- Nicolas Carlotto
- Laboratorio de Agrobiotecnología, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET-UBA), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sonia Wirth
- Laboratorio de Agrobiotecnología, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET-UBA), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolas Furman
- Laboratorio de Agrobiotecnología, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET-UBA), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nazarena Ferreyra Solari
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Federico Ariel
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Ken Kobayashi
- Laboratorio de Agrobiotecnología, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET-UBA), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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50
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Weis BL, Kovacevic J, Missbach S, Schleiff E. Plant-Specific Features of Ribosome Biogenesis. TRENDS IN PLANT SCIENCE 2015; 20:729-740. [PMID: 26459664 DOI: 10.1016/j.tplants.2015.07.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/19/2015] [Accepted: 07/15/2015] [Indexed: 05/03/2023]
Abstract
The biogenesis of eukaryotic ribosomes is a fundamental process involving hundreds of ribosome biogenesis factors (RBFs) in three compartments of the cell, namely the nucleolus, nucleus, and cytoplasm. Many RBFs are involved in the processing of the primary ribosomal (r)RNA transcript, in which three of the four rRNAs are imbedded. While pre-rRNA processing is well described for yeast and mammals, a detailed processing scheme for plants is lacking. Here, we discuss the emerging scheme of pre-rRNA processing in Arabidopsis thaliana in comparison to other eukaryotes, with a focus on plant characteristics. In addition, we highlight the impact of the ribosome and its biogenesis on developmental processes because common phenotypes can be observed for ribosomal protein and RBF mutants.
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Affiliation(s)
- Benjamin L Weis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Jelena Kovacevic
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Sandra Missbach
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Current address: Sanofi-Aventis GmbH, Industriepark Höchst, K703, 65926 Frankfurt am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Cluster of Excellence Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchman Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
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