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Barré-Villeneuve C, Azevedo-Favory J. R-Methylation in Plants: A Key Regulator of Plant Development and Response to the Environment. Int J Mol Sci 2024; 25:9937. [PMID: 39337424 PMCID: PMC11432338 DOI: 10.3390/ijms25189937] [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: 08/23/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Although arginine methylation (R-methylation) is one of the most important post-translational modifications (PTMs) conserved in eukaryotes, it has not been studied to the same extent as phosphorylation and ubiquitylation. Technical constraints, which are in the process of being resolved, may partly explain this lack of success. Our knowledge of R-methylation has recently evolved considerably, particularly in metazoans, where misregulation of the enzymes that deposit this PTM is implicated in several diseases and cancers. Indeed, the roles of R-methylation have been highlighted through the analyses of the main actors of this pathway: the PRMT writer enzymes, the TUDOR reader proteins, and potential "eraser" enzymes. In contrast, R-methylation has been much less studied in plants. Even so, it has been shown that R-methylation in plants, as in animals, regulates housekeeping processes such as transcription, RNA silencing, splicing, ribosome biogenesis, and DNA damage. R-methylation has recently been highlighted in the regulation of membrane-free organelles in animals, but this role has not yet been demonstrated in plants. The identified R-met targets modulate key biological processes such as flowering, shoot and root development, and responses to abiotic and biotic stresses. Finally, arginine demethylases activity has mostly been identified in vitro, so further studies are needed to unravel the mechanism of arginine demethylation.
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Affiliation(s)
- Clément Barré-Villeneuve
- Crop Biotechnics, Department of Biosystems, KU Leuven, 3000 Leuven, Belgium
- KU Leuven Plant Institute (LPI), KU Leuven, 3000 Leuven, Belgium
| | - Jacinthe Azevedo-Favory
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, UMR 5096, 66860 Perpignan, France
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Zhu Q, Ahmad A, Shi C, Tang Q, Liu C, Ouyang B, Deng Y, Li F, Cao X. Protein arginine methyltransferase 6 mediates antiviral immunity in plants. Cell Host Microbe 2024; 32:1566-1578.e5. [PMID: 39106871 DOI: 10.1016/j.chom.2024.07.014] [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: 10/02/2023] [Revised: 04/19/2024] [Accepted: 07/12/2024] [Indexed: 08/09/2024]
Abstract
Viral suppressor RNA silencing (VSR) is essential for successful infection. Nucleotide-binding and leucine-rich repeat (NLR)-based and autophagy-mediated immune responses have been reported to target VSR as counter-defense strategies. Here, we report a protein arginine methyltransferase 6 (PRMT6)-mediated defense mechanism targeting VSR. The knockout and overexpression of PRMT6 in tomato plants lead to enhanced and reduced disease symptoms, respectively, during tomato bush stunt virus (TBSV) infection. PRMT6 interacts with and inhibits the VSR function of TBSV P19 by methylating its key arginine residues R43 and R115, thereby reducing its dimerization and small RNA-binding activities. Analysis of the natural tomato population reveals that two major alleles associated with high and low levels of PRMT6 expression are significantly associated with high and low levels of viral resistance, respectively. Our study establishes PRMT6-mediated arginine methylation of VSR as a mechanism of plant immunity against viruses.
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Affiliation(s)
- Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ayaz Ahmad
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Tang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunyan Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Ouyang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Maekawa S, Nishikawa I, Horiguchi G. Impaired inosine monophosphate dehydrogenase leads to plant-specific ribosomal stress responses in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01578-5. [PMID: 39235732 DOI: 10.1007/s10265-024-01578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/23/2024] [Indexed: 09/06/2024]
Abstract
Nucleotides are the building blocks of living organisms and their biosynthesis must be tightly regulated. Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in GTP synthesis that is essential for biological activities, such as RNA synthesis. In animals, the suppression of IMPDH function causes ribosomal stress (also known as nucleolar stress), a disorder in ribosome biogenesis that results in cell proliferation defects and apoptosis. Despite its importance, plant IMPDH has not been analyzed in detail. Therefore, we analyzed the phenotypes of mutants of the two IMPDH genes in Arabidopsis thaliana and investigated their relationship with ribosomal stress. Double mutants of IMPDH1 and IMPDH2 were lethal, and only the impdh2 mutants showed growth defects and transient chlorophyll deficiency. These results suggested that IMPDH1 and IMPDH2 are redundant and essential, whereas IMPDH2 has a crucial role. In addition, the impdh2 mutants showed a reduction in nucleolus size and resistance to several translation inhibitors, which is a known response to ribosomal stress. Furthermore, the IMPDH1/impdh1 impdh2 mutants showed more severe growth defects and phenotypes such as reduced plastid rRNA levels and abnormal processing patterns than the impdh2 mutants. Finally, multiple mutations of impdh with as2, which has abnormal leaf polarity, caused the development of needle-like leaves because of the enhancement of the as2 phenotype, which is a typical effect observed in mutants of genes involved in ribosome biogenesis. These results indicated that IMPDH is closely related to ribosome biogenesis, and that mutations in the genes lead to not only known responses to ribosomal stress, but also plant-specific responses.
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Affiliation(s)
- Shugo Maekawa
- Institute of Natural Sciences, Senshu University, Higashimita 2-1-1, Tama, Kawasaki, Kanagawa, 214-8580, Japan.
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, 171-8501, Japan.
| | - Ikuto Nishikawa
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, 171-8501, Japan
- Medical Institute of Bioregulation, Kyushu University, Fukuoka City, Fukuoka, 812-8582, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, 171-8501, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo, 171-8501, Japan
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Wang L, Zhu Y, Jiang J, Tan G, Ma Q, Zhang H. Dynamic changes in the levels of metabolites and endogenous hormones during the germination of Zanthoxylum nitidum (Roxb.) DC. Seeds. PLANT SIGNALING & BEHAVIOR 2023; 18:2251750. [PMID: 37639213 PMCID: PMC10464536 DOI: 10.1080/15592324.2023.2251750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
Accumulating experimental data have shown that endogenous hormones play important roles in regulating seed dormancy and germination. Zanthoxylum nitidum is a medicinal plant that propagates via seeds, which require a long dormancy period for normal germination, and complex changes in metabolites occur during the germination process. However, the regulatory network of endogenous hormones and metabolites during the germination of Z. nitidum seeds remains unclear. This study investigated the dynamic changes in the levels of metabolites and endogenous hormones during the germination of Z. nitidum seeds. The results revealed an increase in the levels of gibberellin 3 (GA3), 12-oxophytodienoic acid (OPDA), 1-aminocyclopropane-1-carboxylic acid (ACC) and trans-zeatin (TZ) and decrease in the levels of abscisic acid (ABA), jasmonic acid (JA), N-[(-)-jasmonoyl]-(S)-isoleucine (JA-Ile) and trans-zeatin riboside (TZR). Overall, 112 differential metabolites (DAMs) were screened from 3 seed samples (Sa, Sb and Sc), most of which are related to primary metabolism. A total of 16 DAMs (including 3 monosaccharides, 3 phosphate lipids, 3 carboxylic acids, 1 amino acid, 2 pyrimidines, and 4 nucleotides) were identified in the three sample comparison pairs (Sa vs Sb, Sa vs Sc, and Sb vs Sc); these DAMs were significantly enriched in purine metabolism; glycerophospholipid metabolism, citrate cycle (TCA cycle), alanine, aspartate and glutamate metabolism and pyruvate metabolism. OPDA, ACC and GAs were significantly positively correlated with upregulated metabolites, whereas ABA and JA were significantly positively correlated with downregulated metabolites. Finally, a hypothetical metabolic network of endogenous hormones that regulate seed germination was constructed. This study deepens our understanding of the importance of endogenous hormonal profiles that mediate seed germination.
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Affiliation(s)
- Liang Wang
- Research and Development Center, China Resources Sanjiu Medical & Pharmaceutical CO., LTD., Shenzhen, China
| | - Yanxia Zhu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Key Laboratory for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jianping Jiang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Key Laboratory for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guiyu Tan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Key Laboratory for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qing Ma
- Research and Development Center, China Resources Sanjiu Medical & Pharmaceutical CO., LTD., Shenzhen, China
| | - Hongsheng Zhang
- Research and Development Center, China Resources Sanjiu Medical & Pharmaceutical CO., LTD., Shenzhen, China
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Zu X, Luo L, Wang Z, Gong J, Yang C, Wang Y, Xu C, Qiao X, Deng X, Song X, Chen C, Tan BC, Cao X. A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice. Nat Commun 2023; 14:6789. [PMID: 37880207 PMCID: PMC10600133 DOI: 10.1038/s41467-023-42269-4] [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: 01/16/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.
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Affiliation(s)
- Xiaofeng Zu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lilan Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Gong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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Yi X, Yang D, Xu X, Wang Y, Guo Y, Zhang M, Wang Y, He Y, Zhu J. Cold plasma pretreatment reinforces the lignocellulose-derived aldehyde inhibitors tolerance and bioethanol fermentability for Zymomonas mobilis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:102. [PMID: 37322470 DOI: 10.1186/s13068-023-02354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lignocellulose-derived aldehyde inhibitors seriously blocked the biorefinery of biofuels and biochemicals. To date, the economic production of lignocellulose-based products heavily relied on high productivities of fermenting strains. However, it was expensive and time-consuming for the achievable rational modification to strengthen stress tolerance robustness of aldehyde inhibitors. Here, it aimed to improve aldehyde inhibitors tolerance and cellulosic bioethanol fermentability for the chassis Zymomonas mobilis ZM4 pretreated using energy-efficient and eco-friendly cold plasma. RESULTS It was found that bioethanol fermentability was weaker in CSH (corn stover hydrolysates) than that in synthetic medium for Z. mobilis, and thus was attributed to the inhibition of the lignocellulose-derived aldehyde inhibitors in CSH. Convincingly, it further confirmed that the mixed aldehydes severely decreased bioethanol accumulation through additional aldehydes supplementary assays in synthetic medium. After assayed under different processing time (10-30 s), discharge power (80-160 W), and working pressure (120-180 Pa) using cold atmosphere plasma (CAP), it achieved the increased bioethanol fermentability for Z. mobilis after pretreated at the optimized parameters (20 s, 140 W and 165 Pa). It showed that cold plasma brought about three mutation sites including ZMO0694 (E220V), ZMO0843 (L471L) and ZMO0843 (P505H) via Genome resequencing-based SNPs (single nucleotide polymorphisms). A serial of differentially expressed genes (DEGs) were further identified as the potential contributors for stress tolerance via RNA-Seq sequencing, including ZMO0253 and ZMO_RS09265 (type I secretion outer membrane protein), ZMO1941 (Type IV secretory pathway protease TraF-like protein), ZMOr003 and ZMOr006 (16S ribosomal RNA), ZMO0375 and ZMO0374 (levansucrase) and ZMO1705 (thioredoxins). It enriched cellular process, followed by metabolic process and single-organism process for biological process. For KEGG analysis, the mutant was also referred to starch and sucrose metabolism, galactose metabolism and two-component system. Finally, but interestingly, it simultaneously achieved the enhanced stress tolerance capacity of aldehyde inhibitors and bioethanol fermentability in CSH for the mutant Z. mobilis. CONCLUSIONS Of several candidate genetic changes, the mutant Z. mobilis treated with cold plasma was conferred upon the facilitated aldehyde inhibitors tolerance and bioethanol production. This work would provide a strain biocatalyst for the efficient production of lignocellulosic biofuels and biochemicals.
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Affiliation(s)
- Xia Yi
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, 213164, China.
- Changzhou Key Laboratory of Biomass Green, Safe & High Value Utilization Technology, Changzhou University, Changzhou, 213164, Jiangsu, China.
| | - Dong Yang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Xiaoyan Xu
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Youjun Wang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yan Guo
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Meng Zhang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yilong Wang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yucai He
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China.
| | - Jie Zhu
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, 213164, China.
- Changzhou Key Laboratory of Biomass Green, Safe & High Value Utilization Technology, Changzhou University, Changzhou, 213164, Jiangsu, China.
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China.
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Landry-Voyer AM, Mir Hassani Z, Avino M, Bachand F. Ribosomal Protein uS5 and Friends: Protein-Protein Interactions Involved in Ribosome Assembly and Beyond. Biomolecules 2023; 13:biom13050853. [PMID: 37238722 DOI: 10.3390/biom13050853] [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: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosomal proteins are fundamental components of the ribosomes in all living cells. The ribosomal protein uS5 (Rps2) is a stable component of the small ribosomal subunit within all three domains of life. In addition to its interactions with proximal ribosomal proteins and rRNA inside the ribosome, uS5 has a surprisingly complex network of evolutionarily conserved non-ribosome-associated proteins. In this review, we focus on a set of four conserved uS5-associated proteins: the protein arginine methyltransferase 3 (PRMT3), the programmed cell death 2 (PDCD2) and its PDCD2-like (PDCD2L) paralog, and the zinc finger protein, ZNF277. We discuss recent work that presents PDCD2 and homologs as a dedicated uS5 chaperone and PDCD2L as a potential adaptor protein for the nuclear export of pre-40S subunits. Although the functional significance of the PRMT3-uS5 and ZNF277-uS5 interactions remain elusive, we reflect on the potential roles of uS5 arginine methylation by PRMT3 and on data indicating that ZNF277 and PRMT3 compete for uS5 binding. Together, these discussions highlight the complex and conserved regulatory network responsible for monitoring the availability and the folding of uS5 for the formation of 40S ribosomal subunits and/or the role of uS5 in potential extra-ribosomal functions.
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Affiliation(s)
- Anne-Marie Landry-Voyer
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Zabih Mir Hassani
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mariano Avino
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - François Bachand
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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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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Guo Z, Wang X, Li Y, Xing A, Wu C, Li D, Wang C, de Bures A, Zhang Y, Guo S, Sáez-Vasquez J, Shen Z, Hu Z. Arabidopsis SMO2 modulates ribosome biogenesis by maintaining the RID2 abundance during organ growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:96-109. [PMID: 36705084 DOI: 10.1111/tpj.16121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ribosome biogenesis is a process of making ribosomes that is tightly linked with plant growth and development. Here, through a suppressor screen for the smo2 mutant, we found that lack of a ribosomal stress response mediator, ANAC082 partially restored growth defects of the smo2 mutant, indicating SMO2 is required for the repression of nucleolar stress. Consistently, the smo2 knock-out mutant exhibited typical phenotypes characteristic of ribosome biogenesis mutants, such as pointed leaves, aberrant leaf venation, disrupted nucleolar structure, abnormal distribution of rRNA precursors, and enhanced tolerance to aminoglycoside antibiotics that target ribosomes. SMO2 interacted with ROOT INITIATION DEFECTIVE 2 (RID2), a methyltransferase-like protein required for pre-rRNA processing. SMO2 enhanced RID2 solubility in Escherichia coli and the loss of function of SMO2 in plant cells reduced RID2 abundance, which may result in abnormal accumulation of FIBRILLARIN 1 (FIB1) and NOP56, two key nucleolar proteins, in high-molecular-weight protein complex. Taken together, our results characterized a novel plant ribosome biogenesis factor, SMO2 that maintains the abundance of RID2, thereby sustaining ribosome biogenesis during plant organ growth.
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Affiliation(s)
- Zhengfei Guo
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Yan Li
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Aiming Xing
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Daojun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, 442000, Shiyan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Julio Sáez-Vasquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
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10
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Wang Z, Sun J, Zu X, Gong J, Deng H, Hang R, Zhang X, Liu C, Deng X, Luo L, Wei X, Song X, Cao X. Pseudouridylation of chloroplast ribosomal RNA contributes to low temperature acclimation in rice. THE NEW PHYTOLOGIST 2022; 236:1708-1720. [PMID: 36093745 DOI: 10.1111/nph.18479] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown. Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss-function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature. We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre-rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre-rRNAs are observed in ospus1-1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1-1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress-responsive state, preventing excess reactive oxygen species accumulation. Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in crop improvement.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Zu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Gong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongjing Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Runlai Hang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lilan Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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11
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Mo C, Xie C, Wang G, Tian T, Liu J, Zhu C, Xiao X, Xiao Y. Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi. Nucleic Acids Res 2021; 49:12358-12376. [PMID: 34792171 PMCID: PMC8643696 DOI: 10.1093/nar/gkab1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/14/2022] Open
Abstract
The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.
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Affiliation(s)
- Chenmi Mo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chong Xie
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Gaofeng Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Tian Tian
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Juan Liu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chunxiao Zhu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yannong Xiao
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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