1
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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2
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Cao Y, Wang J, Wu S, Yin X, Shu J, Dai X, Liu Y, Sun L, Zhu D, Deng XW, Ye K, Qian W. The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. THE PLANT CELL 2022; 34:4173-4190. [PMID: 36005862 PMCID: PMC9614442 DOI: 10.1093/plcell/koac265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs (ncRNAs) that guide chemical modifications of structural RNAs, which are essential for ribosome assembly and function in eukaryotes. Although numerous snoRNAs have been identified in plants by high-throughput sequencing, the biological functions of most of these snoRNAs remain unclear. Here, we identified box C/D SnoR28.1s as important regulators of plant growth and development by screening a CRISPR/Cas9-generated ncRNA deletion mutant library in Arabidopsis thaliana. Deletion of the SnoR28.1 locus, which contains a cluster of three genes producing SnoR28.1s, resulted in defects in root and shoot growth. SnoR28.1s guide 2'-O-ribose methylation of 25S rRNA at G2396. SnoR28.1s facilitate proper and efficient pre-rRNA processing, as the SnoR28.1 deletion mutants also showed impaired ribosome assembly and function, which may account for the growth defects. SnoR28 contains a 7-bp antisense box, which is required for 2'-O-ribose methylation of 25S rRNA at G2396, and an 8-bp extra box that is complementary to a nearby rRNA methylation site and is partially responsible for methylation of G2396. Both of these motifs are required for proper and efficient pre-rRNA processing. Finally, we show that SnoR28.1s genetically interact with HIDDEN TREASURE2 and NUCLEOLIN1. Our results advance our understanding of the roles of snoRNAs in Arabidopsis.
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Affiliation(s)
- Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, 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
| | - Songlin Wu
- Key Laboratory of RNA Biology, 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
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jia Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, 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
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
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3
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Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lisón P, Taoka M, Amunts A. Cryo-EM structure and rRNA modification sites of a plant ribosome. PLANT COMMUNICATIONS 2022; 3:100342. [PMID: 35643637 PMCID: PMC9483110 DOI: 10.1016/j.xplc.2022.100342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/07/2022] [Accepted: 05/25/2022] [Indexed: 05/25/2023]
Abstract
Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
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Affiliation(s)
- Patrick Cottilli
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden.
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4
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Streit D, Schleiff E. The Arabidopsis 2'-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:684626. [PMID: 34381476 PMCID: PMC8351944 DOI: 10.3389/fpls.2021.684626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2'-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
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5
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Wu S, Wang Y, Wang J, Li X, Li J, Ye K. Profiling of RNA ribose methylation in Arabidopsis thaliana. Nucleic Acids Res 2021; 49:4104-4119. [PMID: 33784398 PMCID: PMC8053127 DOI: 10.1093/nar/gkab196] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/20/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic rRNAs and snRNAs are decorated with abundant 2′-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with multiple specificities as shown in yeast. We found that C/D snoRNAs frequently form extra pairs with nearby sequences of methylation sites, potentially facilitating the substrate binding. Chloroplast and mitochondrial rRNAs contain five almost identical methylation sites, including two novel sites mediating ribosomal subunit joining. Deletion of FIB1 or FIB2 gene reduced the accumulation of C/D snoRNA and rRNA methylation with FIB1 playing a bigger role in methylation. Our data reveal the comprehensive 2′-O-methylation maps for Arabidopsis rRNAs and snRNAs and would facilitate study of their function and biosynthesis.
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Affiliation(s)
- Songlin Wu
- Key Laboratory of RNA Biology, 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
| | - Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, 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
| | - Xilong Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, 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
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6
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Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans 2021; 48:645-656. [PMID: 32267490 PMCID: PMC7200641 DOI: 10.1042/bst20191046] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
Identified five decades ago amongst the most abundant cellular RNAs, small nucleolar RNAs (snoRNAs) were initially described as serving as guides for the methylation and pseudouridylation of ribosomal RNA through direct base pairing. In recent years, however, increasingly powerful high-throughput genomic approaches and strategies have led to the discovery of many new members of the family and surprising diversity in snoRNA functionality and mechanisms of action. SnoRNAs are now known to target RNAs of many biotypes for a wider range of modifications, interact with diverse binding partners, compete with other binders for functional interactions, recruit diverse players to targets and affect protein function and accessibility through direct interaction. This mini-review presents the continuing characterization of the snoRNome through the identification of new snoRNA members and the discovery of their mechanisms of action, revealing a highly versatile noncoding family playing central regulatory roles and connecting the main cellular processes.
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7
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Azevedo-Favory J, Gaspin C, Ayadi L, Montacié C, Marchand V, Jobet E, Rompais M, Carapito C, Motorin Y, Sáez-Vásquez J. Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants. RNA Biol 2021; 18:1760-1777. [PMID: 33596769 PMCID: PMC8583080 DOI: 10.1080/15476286.2020.1869892] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In all eukaryotic cells, the most abundant modification of ribosomal RNA (rRNA) is methylation at the ribose moiety (2ʹ-O-methylation). Ribose methylation at specific rRNA sites is guided by small nucleolar RNAs (snoRNAs) of C/D-box type (C/D snoRNA) and achieved by the methyltransferase Fibrillarin (FIB). Here we used the Illumina-based RiboMethSeq approach for mapping rRNA 2ʹ-O-methylation sites in A. thaliana Col-0 (WT) plants. This analysis detected novel C/D snoRNA-guided rRNA 2ʹ-O-methylation positions and also some orphan sites without a matching C/D snoRNA. Furthermore, immunoprecipitation of Arabidopsis FIB2 identified and demonstrated expression of C/D snoRNAs corresponding to majority of mapped rRNA sites. On the other hand, we show that disruption of Arabidopsis Nucleolin 1 gene (NUC1), encoding a major nucleolar protein, decreases 2ʹ-O-methylation at specific rRNA sites suggesting functional/structural interconnections of 2ʹ-O-methylation with nucleolus organization and plant development. Finally, based on our findings and existent database sets, we introduce a new nomenclature system for C/D snoRNA in Arabidopsis plants.
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Affiliation(s)
- J Azevedo-Favory
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
| | - C Gaspin
- Université Fédérale de Toulouse, INRAE, MIAT, 31326, Castanet-Tolosan, France.,Université Fédérale de Toulouse, INRAE, BioinfOmics, Genotoul Bioinformatics facility, 31326
| | - L Ayadi
- Université de Lorraine, CNRS, INSERM, IBSLor, (UMS2008/US40), Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France.,Université de Lorraine, CNRS, IMoPA (UMR7365), F-54000 Nancy, France
| | - C Montacié
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
| | - V Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor, (UMS2008/US40), Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France
| | - E Jobet
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
| | - 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
| | - Y Motorin
- Université de Lorraine, CNRS, INSERM, IBSLor, (UMS2008/US40), Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France.,Université de Lorraine, CNRS, IMoPA (UMR7365), F-54000 Nancy, France
| | - J Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
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8
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Bousquet L, Hemon C, Malburet P, Bucchini F, Vandepoele K, Grimsley N, Moreau H, Echeverria M. The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies. NAR Genom Bioinform 2020; 2:lqaa080. [PMID: 33575626 PMCID: PMC7671301 DOI: 10.1093/nargab/lqaa080] [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: 05/07/2020] [Revised: 08/31/2020] [Accepted: 09/17/2020] [Indexed: 11/14/2022] Open
Abstract
The small nucleolar RNAs (snoRNAs), essential for ribosome biogenesis, constitute a major family of medium-size noncoding RNAs (mncRNAs) in all eukaryotes. We present here, for the first time in a marine unicellular alga, the characterization of the snoRNAs family in Ostreococcus tauri, the smallest photosynthetic eukaryote. Using a transcriptomic approach, we identified 131 O. tauri snoRNAs (Ot–snoRNA) distributed in three classes: the C/D snoRNAs, the H/ACA snoRNAs and the MRP RNA. Their genomic organization revealed a unique combination of both the intronic organization of animals and the polycistronic organization of plants. Remarkably, clustered genes produced Ot–snoRNAs with unusual structures never previously described in plants. Their abundances, based on quantification of reads and northern blots, showed extreme differences in Ot–snoRNA accumulation, mainly determined by their differential stability. Most of these Ot–snoRNAs were predicted to target rRNAs or snRNAs. Seventeen others were orphan Ot–snoRNAs that would not target rRNA. These were specific to O. tauri or Mamiellophyceae and could have functions unrelated to ribosome biogenesis. Overall, these data reveal an ‘evolutionary response’ adapted to the extreme compactness of the O. tauri genome that accommodates the essential Ot–snoRNAs, developing multiple strategies to optimize their coordinated expression with a minimal cost on regulatory circuits.
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Affiliation(s)
- Laurie Bousquet
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Claire Hemon
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Paul Malburet
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - François Bucchini
- Department of Plant Systems Biology,VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology,VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Bioinformatic Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Nigel Grimsley
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Hervé Moreau
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Manuel Echeverria
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
- Département de Biologie, Université de Perpignan via Domitia, 66860 Perpignan Cedex, France
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9
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Streit D, Shanmugam T, Garbelyanski A, Simm S, Schleiff E. The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1016. [PMID: 32806552 PMCID: PMC7464842 DOI: 10.3390/plants9081016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Thiruvenkadam Shanmugam
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Asen Garbelyanski
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
- Institute of Bioinformatics, University Medicine Greifswald, D-17475 Greifswald, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
- Frankfurt Institute of Advanced Studies (FIAS), D-60438 Frankfurt am Main, Germany
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10
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Ayadi L, Galvanin A, Pichot F, Marchand V, Motorin Y. RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:253-269. [PMID: 30572123 DOI: 10.1016/j.bbagrm.2018.11.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023]
Abstract
Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.
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Affiliation(s)
- Lilia Ayadi
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Adeline Galvanin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Florian Pichot
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Virginie Marchand
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France.
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11
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Moore AN, McWatters DC, Hudson AJ, Russell AG. RNA-Seq employing a novel rRNA depletion strategy reveals a rich repertoire of snoRNAs in Euglena gracilis including box C/D and Ψ-guide RNAs targeting the modification of rRNA extremities. RNA Biol 2018; 15:1309-1318. [PMID: 30252600 PMCID: PMC6284569 DOI: 10.1080/15476286.2018.1526561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/21/2018] [Accepted: 09/16/2018] [Indexed: 01/06/2023] Open
Abstract
Previous mRNA transcriptome studies of Euglena gracilis have shown that this organism possesses a large and diverse complement of protein coding genes; however, the study of non-coding RNA classes has been limited. The natural extensive fragmentation of the E. gracilis large subunit ribosomal RNA presents additional barriers to the identification of non-coding RNAs as size-selected small RNA libraries will be dominated by rRNA sequences. In this study we have developed a strategy to significantly reduce rRNA amplification prior to RNA-Seq analysis thereby producing a ncRNA library allowing for the identification of many new E. gracilis small RNAs. Library analysis reveals 113 unique new small nucleolar (sno) RNAs and a large collection of snoRNA isoforms, as well as the first significant collection of nuclear tRNAs in this organism. A 3' end AGAUGN consensus motif and conserved structural features can now be defined for E. gracilis pseudouridine guide RNAs. snoRNAs of both classes were identified that target modification of the 3' extremities of rRNAs utilizing predicted base-pairing interactions with internally transcribed spacers (ITS), providing insight into the timing of steps in rRNA maturation. Cumulatively, this represents the most comprehensive analysis of small ncRNAs in Euglena gracilis to date.
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Affiliation(s)
- Ashley N. Moore
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - David C. McWatters
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Andrew J. Hudson
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Anthony G. Russell
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
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12
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Patra Bhattacharya D, Canzler S, Kehr S, Hertel J, Grosse I, Stadler PF. Phylogenetic distribution of plant snoRNA families. BMC Genomics 2016; 17:969. [PMID: 27881081 PMCID: PMC5122169 DOI: 10.1186/s12864-016-3301-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3301-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deblina Patra Bhattacharya
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.,Institut für Informatik, Halle (Saale), D-06120, Germany
| | - Sebastian Canzler
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany
| | - Jana Hertel
- Young Investigators Group Bioinformatics & Transcriptomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, D-04318, Germany
| | - Ivo Grosse
- Institut für Informatik, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, D-04103, Germany. .,Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, Leipzig, A-1090, Germany. .,Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Copenhagen, Denmark. .,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. .,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.
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13
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Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A, Szweykowska-Kulinska Z, Echeverria M, Karlowski WM. Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. BMC Genomics 2015; 16:1009. [PMID: 26607788 PMCID: PMC4660826 DOI: 10.1186/s12864-015-2221-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022] Open
Abstract
Background In the past few decades, non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression in eukaryotes. Most studies of ncRNAs in plants have focused on the identification of silencing microRNAs (miRNAs) and small interfering RNAs (siRNAs). Another important family of ncRNAs that has been well characterized in plants is the small nucleolar RNAs (snoRNAs) and the related small Cajal body-specific RNAs (scaRNAs). Both target chemical modifications of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In plants, the snoRNA genes are organized in clusters, transcribed by RNA Pol II from a common promoter and subsequently processed into mature molecules. The promoter regions of snoRNA polycistronic genes in plants are highly enriched in two conserved cis-regulatory elements (CREs), Telo-box and Site II, which coordinate the expression of snoRNAs and ribosomal protein coding genes throughout the cell cycle. Results In order to identify novel ncRNA genes, we have used the snoRNA Telo-box/Site II motifs combination as a functional promoter indicator to screen the Arabidopsis genome. The predictions generated by this process were tested by detailed exploration of available RNA-Seq and expression data sets and experimental validation. As a result, we have identified several snoRNAs, scaRNAs and 'orphan' snoRNAs. We also show evidence for 16 novel ncRNAs that lack similarity to any reported RNA family. Finally, we have identified two dicistronic genes encoding precursors that are processed to mature snoRNA and miRNA molecules. We discuss the evolutionary consequences of this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes. Conclusions We present an alternative computational approach for non-coding RNA detection. Instead of depending on sequence or structure similarity in the whole genome screenings, we have explored the properties of promoter regions of well-characterized ncRNAs. Interestingly, besides expected ncRNAs predictions we were also able to recover single precursor arrangement for snoRNA-miRNA. Accompanied by analyses performed on rice sequences, we conclude that such arrangement might have interesting functional and evolutionary consequences and discuss this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2221-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ge Qu
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Shu-Yi Yang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd. Sec. 2, Taipei, 115, Taiwan.
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd. Sec. 2, Taipei, 115, Taiwan.
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Manuel Echeverria
- Faculté des Sciences, Université de Perpignan via Domitia, 52, Av Paul Alduy, Perpignan, 66860, France.
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
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14
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Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:708. [PMID: 25566282 PMCID: PMC4274896 DOI: 10.3389/fpls.2014.00708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/26/2014] [Indexed: 05/11/2023]
Abstract
High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we introduce an extension of this system to plant short non-coding RNAs (sncRNAs). It includes major modifications to cope with plant-specific sncRNA processing. The current version of plantDARIO covers analyses of mapping files, small RNA-seq quality control, expression analyses of annotated sncRNAs, including the prediction of novel miRNAs and snoRNAs from unknown expressed loci and expression analyses of user-defined loci. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. The web tool links to a plant specific visualization browser to display the read distribution of the analyzed sample. The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group. The plantDARIO website can be accessed at http://plantdario.bioinf.uni-leipzig.de/.
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Affiliation(s)
- Deblina Patra
- Institut für Informatik, Martin-Luther-Universität Halle-WittenbergHalle (Saale), Germany
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- ecSeq BioinformaticsLeipzig, Germany
| | - David Langenberger
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- ecSeq BioinformaticsLeipzig, Germany
| | - Gerhard Steger
- Institut für Pysikalische Biologie, Heinrich-Heine-UniversitätDüsseldorf, Germany
| | - Ivo Grosse
- Institut für Informatik, Martin-Luther-Universität Halle-WittenbergHalle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
- Max Planck Institute for Mathematics in the SciencesLeipzig, Germany
- Fraunhofer Institute for Cell Therapy and ImmunologyLeipzig, Germany
- Department of Theoretical Chemistry of the University of ViennaVienna, Austria
- Center for RNA in Technology and Health, University of CopenhagenFrederiksberg, Denmark
- Santa Fe InstituteSanta Fe, USA
- *Correspondence: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany e-mail:
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15
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Liu N, Xiao B, Ren HY, Tang ZL, Li K. Systematic identification and characterization of porcine snoRNAs: structural, functional and developmental insights. Anim Genet 2012; 44:24-33. [DOI: 10.1111/j.1365-2052.2012.02363.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Nan Liu
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Bang Xiao
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Hong-Yan Ren
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Zhong-Lin Tang
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Kui Li
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
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16
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Larsen LHG, Rasmussen A, Giessing AMB, Jogl G, Kirpekar F. Identification and characterization of the Thermus thermophilus 5-methylcytidine (m5C) methyltransferase modifying 23 S ribosomal RNA (rRNA) base C1942. J Biol Chem 2012; 287:27593-600. [PMID: 22711535 DOI: 10.1074/jbc.m112.376160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylation of cytidines at carbon-5 is a common posttranscriptional RNA modification encountered across all domains of life. Here, we characterize the modifications of C1942 and C1962 in Thermus thermophilus 23 S rRNA as 5-methylcytidines (m(5)C) and identify the two associated methyltransferases. The methyltransferase modifying C1942, named RlmO, has not been characterized previously. RlmO modifies naked 23 S rRNA, but not the assembled 50 S subunit or 70 S ribosomes. The x-ray crystal structure of this enzyme in complex with the S-adenosyl-l-methionine cofactor at 1.7 Å resolution confirms that RlmO is structurally related to other m(5)C rRNA methyltransferases. Key residues in the active site are located similar to the further distant 5-methyluridine methyltransferase RlmD, suggestive of a similar enzymatic mechanism. RlmO homologues are primarily found in mesophilic bacteria related to T. thermophilus. In accordance, we find that growth of the T. thermophilus strain with an inactivated C1942 methyltransferase gene is not compromised at non-optimal temperatures.
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Affiliation(s)
- Line H G Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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17
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Goyal RK, Kumar V, Shukla V, Mattoo R, Liu Y, Chung SH, Giovannoni JJ, Mattoo AK. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). PLANTA 2012; 235:453-71. [PMID: 21947620 DOI: 10.1007/s00425-011-1518-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/05/2011] [Indexed: 05/03/2023]
Abstract
Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.
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Affiliation(s)
- Ravinder K Goyal
- US Department of Agriculture, The Henry A. Wallace Beltsville Agricultural Research Center, Agriculture Research Service, Beltsville, MD 20705-2350, USA
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18
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Moore AN, Russell AG. Clustered organization, polycistronic transcription, and evolution of modification-guide snoRNA genes in Euglena gracilis. Mol Genet Genomics 2011; 287:55-66. [PMID: 22134850 DOI: 10.1007/s00438-011-0662-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/19/2011] [Indexed: 10/15/2022]
Abstract
Previous studies have shown that the eukaryotic microbe Euglena gracilis contains an unusually large assortment of small nucleolar RNAs (snoRNAs) and ribosomal RNA (rRNA) modification sites. However, little is known about the evolutionary mechanisms contributing to this situation. In this study, we have examined the organization and evolution of snoRNA genes in Euglena with the additional objective of determining how these properties relate to the rRNA modification pattern in this protist. We have identified and extensively characterized a clustered pattern of genes encoding previously biochemically isolated snoRNA sequences in E. gracilis. We show that polycistronic transcription is a prevalent snoRNA gene expression strategy in this organism. Further, we have identified 121 new snoRNA coding regions through sequence analysis of these clusters. We have identified an E. gracilis U14 snoRNA homolog clustered with modification-guide snoRNA genes. The U14 snoRNAs in other eukaryotic organisms examined to date typically contain both a modification and a processing domain. E. gracilis U14 lacks the modification domain but retains the processing domain. Our analysis of U14 structure and evolution in Euglena and other eukaryotes allows us to propose a model for its evolution and suggest its processing role may be its more important function, explaining its conservation in many eukaryotes. The preponderance of apparent small and larger-scale duplication events in the genomic regions we have characterized in Euglena provides a mechanism for the generation of the unusually diverse collection and abundance of snoRNAs and modified rRNA sites. Our findings provide the framework for more extensive whole genome analysis to elucidate whether these snoRNA gene clusters are spread across multiple chromosomes and/or form dense "arrays" at a limited number of chromosomal loci.
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Affiliation(s)
- Ashley N Moore
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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19
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Schnare MN, Gray MW. Complete modification maps for the cytosolic small and large subunit rRNAs of Euglena gracilis: functional and evolutionary implications of contrasting patterns between the two rRNA components. J Mol Biol 2011; 413:66-83. [PMID: 21875598 DOI: 10.1016/j.jmb.2011.08.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
In the protist Euglena gracilis, the cytosolic small subunit (SSU) rRNA is a single, covalently continuous species typical of most eukaryotes; in contrast, the large subunit (LSU) rRNA is naturally fragmented, comprising 14 separate RNA molecules instead of the bipartite (28S+5.8S) eukaryotic LSU rRNA typically seen. We present extensively revised secondary structure models of the E. gracilis SSU and LSU rRNAs and have mapped the positions of all of the modified nucleosides in these rRNAs (88 in SSU rRNA and 262 in LSU rRNA, with only 3 LSU rRNA modifications incompletely characterized). The relative proportions of ribose-methylated nucleosides and pseudouridine (∼60% and ∼35%, respectively) are closely similar in the two rRNAs; however, whereas the Euglena SSU rRNA has about the same absolute number of modifications as its human counterpart, the Euglena LSU rRNA has twice as many modifications as the corresponding human LSU rRNA. The increased levels of rRNA fragmentation and modification in E. gracilis LSU rRNA are correlated with a 3-fold increase in the level of mispairing in helical regions compared to the human LSU rRNA. In contrast, no comparable increase in mispairing is seen in helical regions of the SSU rRNA compared to its homologs in other eukaryotes. In view of the reported effects of both ribose-methylated nucleoside and pseudouridine residues on RNA structure, these correlations lead us to suggest that increased modification in the LSU rRNA may play a role in stabilizing a 'looser' structure promoted by elevated helical mispairing and a high degree of fragmentation.
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Affiliation(s)
- Murray N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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20
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Rodor J, Jobet E, Bizarro J, Vignols F, Carles C, Suzuki T, Nakamura K, Echeverría M. AtNUFIP, an essential protein for plant development, reveals the impact of snoRNA gene organisation on the assembly of snoRNPs and rRNA methylation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:807-819. [PMID: 21261762 DOI: 10.1111/j.1365-313x.2010.04468.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In all eukaryotes, C/D small nucleolar ribonucleoproteins (C/D snoRNPs) are essential for methylation and processing of ribosomal RNAs. They consist of a box C/D small nucleolar RNA (C/D snoRNA) associated with four highly conserved nucleolar proteins. Recent data in HeLa cells and yeast have revealed that assembly of these snoRNPs is directed by NUFIP protein and other auxiliary factors. Nevertheless, the precise function and biological importance of NUFIP and the other assembly factors remains unknown. In plants, few studies have focused on RNA methylation and snoRNP biogenesis. Here, we identify and characterise the AtNUFIP gene that directs assembly of C/D snoRNP. To elucidate the function of AtNUFIP in planta, we characterized atnufip mutants. These mutants are viable but have severe developmental phenotypes. Northern blot analysis of snoRNA accumulation in atnufip mutants revealed a specific degradation of C/D snoRNAs and this situation is correlated with a reduction in rRNA methylation. Remarkably, the impact of AtNUFIP depends on the structure of snoRNA genes: it is essential for the accumulation of those C/D snoRNAs encoded by polycistronic genes, but not by monocistronic or tsnoRNA genes. We propose that AtNUFIP controls the kinetics of C/D snoRNP assembly on nascent precursors to overcome snoRNA degradation of aberrant RNPs. Finally, we show that AtNUFIP has broader RNP targets, controlling the accumulation of scaRNAs that direct methylation of spliceosomal snRNA in Cajal bodies.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Gene Expression Profiling
- Genetic Complementation Test
- Methylation
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutation
- Phenotype
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- RNA Processing, Post-Transcriptional
- RNA Stability
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Ribosomal/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Sequence Alignment
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Affiliation(s)
- Julie Rodor
- Laboratoire Génome et Développement des Plantes, UMR 5096 Université de Perpignan via Domitia - Centre National de la Recherche Scientifique - Institut de Recherche pour le Développement, Perpignan, France
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21
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Sáez-Vásquez J, Gadal O. Genome organization and function: a view from yeast and Arabidopsis. MOLECULAR PLANT 2010; 3:678-690. [PMID: 20601371 DOI: 10.1093/mp/ssq034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Recent progress in understanding higher-order chromatin organization in the nucleus has been considerable. From single gene to chromosome territory, realistic biophysical models can now accurately predict some of the structural feature of cell nuclei. Despite growing evidence of a deterministic nuclear organization, the physiological consequence of spatial genome organization is still unclear. In the simple eukaryotic model, Saccharomyces cerevisiae, clear correlation between gene position and transcription has been established. In this review, we will focus on higher-order chromatin organization in yeast with respect to the nuclear envelope and nucleolus. In Arabidopsis thaliana, a model plant for which we have a complete genome sequence, chromosome territory (CT) arrangement and somatic homologous pairing in interphase nuclei seem to occur randomly. Since chromosomes containing nucleolar organizer regions associate more frequently to form a single nucleolar structure, as in yeast, the nucleolus seems to play a major role in organizing nuclear space. Recent findings have begun to elucidate how plant regulatory factors, such as chromatin remodeling or histone chaperones, affect the chromatin state of ribosomal DNA genes located in two distinct CT arrangements in the nucleus. The functional outcome of yeast nuclear organization allowed us to propose how nuclear organization might contribute to a novel type of epigenetic regulation: the spatial regulation of transcription.
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Affiliation(s)
- Julio Sáez-Vásquez
- LGDP-UMR 5096 CNRS-IRD-Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
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22
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Kim SH, Spensley M, Choi SK, Calixto CPG, Pendle AF, Koroleva O, Shaw PJ, Brown JWS. Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli. Nucleic Acids Res 2010; 38:3054-67. [PMID: 20081206 PMCID: PMC2875012 DOI: 10.1093/nar/gkp1241] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 12/23/2009] [Accepted: 12/23/2009] [Indexed: 11/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.
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Affiliation(s)
- Sang Hyon Kim
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Mark Spensley
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Seung Kook Choi
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Cristiane P. G. Calixto
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Ali F. Pendle
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Olga Koroleva
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Peter J. Shaw
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - John W. S. Brown
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Kyeongki-do 449-728, Korea, Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH and School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
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Samaha H, Delorme V, Pontvianne F, Cooke R, Delalande F, Van Dorsselaer A, Echeverria M, Sáez-Vásquez J. Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:383-398. [PMID: 19891704 DOI: 10.1111/j.1365-313x.2009.04061.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on the structural characterization of a functional U3 snoRNA ribonucleoprotein complex isolated from Brassica oleracea. The BoU3 snoRNP complex (formerly NF D) binds ribosomal DNA (rDNA), specifically cleaves pre-rRNA at the primary cleavage site in vitro and probably links transcription to early pre-rRNA processing in vivo. Using a proteomic approach we have identified 62 proteins in the purified BoU3 snoRNP fraction, including small RNA associated proteins (Fibrillarin, NOP5/Nop58p, Diskerin/Cbf5p, SUS2/PRP8 and CLO/GFA1/sn114p) and 40S ribosomal associated proteins (22 RPS and four ARCA-like proteins). Another major protein group is composed of chaperones/chaperonins (HSP81/TCP-1) and at least one proteasome subunit (RPN1a). Remarkably, RNA-dependent RNA polymerase (RdRP) and Tudor staphylococcal nuclease (TSN) proteins, which have RNA- and/or DNA-associated activities, were also revealed in the complex. Furthermore, three U3 snoRNA variants were identified in the BoU3 snoRNP fraction, notably an evolutionarily conserved and variable stem loop structure located just downstream from the C-box domain of the U3 sequence structures. We conclude that the BoU3 snoRNP complex is mainly required for 40S pre-ribosome synthesis. It is also expected that U3 snoRNA variants and interacting proteins might play a major role in BoU3 snoRNP complex assembly and/or function. This study provides a basis for further investigation of these novel ribonucleoprotein factors and their role in plant ribosome biogenesis.
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Affiliation(s)
- Hala Samaha
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-UPVD, Perpignan France
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24
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Liu N, Xiao ZD, Yu CH, Shao P, Liang YT, Guan DG, Yang JH, Chen CL, Qu LH, Zhou H. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics 2009; 10:515. [PMID: 19895704 PMCID: PMC2780460 DOI: 10.1186/1471-2164-10-515] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/08/2009] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. RESULTS Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. CONCLUSION This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex pattern of methylation guided by box C/D snoRNAs in multicellular fungus than in unicellular yeasts was revealed, indicating the high diversity of post-transcriptional modification guided by snoRNAs in the fungus kingdom.
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Affiliation(s)
- Na Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhen-Dong Xiao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chun-Hong Yu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Peng Shao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yin-Tong Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Dao-Gang Guan
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chun-Long Chen
- Centre National de la Recherche Scientifique (CNRS), UPR 2167, CGM, Gif sur Yvette, 91198, France
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
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Dieci G, Preti M, Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics 2009; 94:83-8. [PMID: 19446021 DOI: 10.1016/j.ygeno.2009.05.002] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/30/2009] [Accepted: 05/07/2009] [Indexed: 11/26/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs - to guide site-specific rRNA modification - is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parma, Italy.
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26
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Chen HM, Wu SH. Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis. Nucleic Acids Res 2009; 37:e69. [PMID: 19357091 PMCID: PMC2685112 DOI: 10.1093/nar/gkp225] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs that direct 2′-O-methylation or pseudouridylation on ribosomal RNAs or spliceosomal small nuclear RNAs. These modifications are needed to modulate the activity of ribosomes and spliceosomes. A comprehensive repertoire of snoRNAs is needed to expand the knowledge of these modifications. The sequences corresponding to snoRNAs in 18–26-nt small RNA sequencing data have been rarely explored and remain as a hidden treasure for snoRNA annotation. Here, we showed the enrichment of small RNAs at Arabidopsis snoRNA termini and developed a computational approach to identify snoRNAs on the basis of this characteristic. The approach successfully uncovered the full-length sequences of 144 known Arabidopsis snoRNA genes, including some snoRNAs with improved 5′- or 3′-end annotation. In addition, we identified 27 and 17 candidates for novel box C/D and box H/ACA snoRNAs, respectively. Northern blot analysis and sequencing data from parallel analysis of RNA ends confirmed the expression and the termini of the newly predicted snoRNAs. Our study especially expanded on the current knowledge of box H/ACA snoRNAs and snoRNA species targeting snRNAs. In this study, we demonstrated that the use of small RNA sequencing data can increase the complexity and the accuracy of snoRNA annotation.
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Affiliation(s)
- Ho-Ming Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
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27
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Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S, Unger R. Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes. BMC Bioinformatics 2008; 9:471. [PMID: 18986541 PMCID: PMC2613932 DOI: 10.1186/1471-2105-9-471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 11/05/2008] [Indexed: 11/12/2022] Open
Abstract
Background Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to pseudouridine on rRNA in trypanosomes, because these organisms have unique H/ACA molecules (termed H/ACA-like) that lack several of the features that characterize H/ACA molecules in most other organisms. Results We present here a computational tool called Psiscan, which was designed to detect H/ACA-like molecules in trypanosomes. We started by analyzing known H/ACA-like molecules and characterized their crucial elements both computationally and experimentally. Next, we set up constraints based on this analysis and additional phylogenic and functional data to rapidly scan three trypanosome genomes (T. brucei, T. cruzi and L. major) for sequences that observe these constraints and are conserved among the species. In the next step, we used minimal energy calculation to select the molecules that are predicted to fold into a lowest energy structure that is consistent with the constraints. In the final computational step, we used a Support Vector Machine that was trained on known H/ACA-like molecules as positive examples and on negative examples of molecules that were identified by the computational analyses but were shown experimentally not to be H/ACA-like molecules. The leading candidate molecules predicted by the SVM model were then subjected to experimental validation. Conclusion The experimental validation showed 11 molecules to be expressed (4 out of 25 in the intermediate stage and 7 out of 19 in the final validation after the machine learning stage). Five of these 11 molecules were further shown to be bona fide H/ACA-like molecules. As snoRNA in trypanosomes are organized in clusters, the new H/ACA-like molecules could be used as starting points to manually search for additional molecules in their neighbourhood. All together this study increased our repertoire by fourteen H/ACA-like and six C/D snoRNAs molecules from T. brucei and L. Major. In addition the experimental analysis revealed that six ncRNA molecules that are expressed are not downregulated in CBF5 silenced cells, suggesting that they have structural features of H/ACA-like molecules but do not have their standard function. We termed this novel class of molecules AGA-like, and we are exploring their function. This study demonstrates the power of tight collaboration between computational and experimental approaches in a combined effort to reveal the repertoire of ncRNA molecles.
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Affiliation(s)
- Inna Myslyuk
- Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel.
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Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters. Genetics 2008; 179:21-30. [PMID: 18493037 DOI: 10.1534/genetics.107.086025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chlamydomonas reinhardtii is a unicellular green alga, the lineage of which diverged from that of land plants >1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 box H/ACA families can potentially guide pseudouridylation at 62 sites. Remarkably, 242 of the snoRNA genes are arranged into 76 clusters, of which 77% consist of homologous genes produced by small local tandem duplications. At least 70 snoRNA gene clusters are found within introns of protein-coding genes. Although not exhaustive, this analysis reveals that C. reinhardtii has the highest number of intronic snoRNA gene clusters among eukaryotes. The prevalence of intronic snoRNA gene clusters in C. reinhardtii is similar to that of rice but in contrast with the one-snoRNA-per-intron organization of vertebrates and fungi and with that of Arabidopsis thaliana in which only a few intronic snoRNA gene clusters were identified. This analysis of C. reinhardtii snoRNA gene organization shows the functional importance of introns in a single-celled organism and provides evolutionary insight into the origin of intron-encoded RNAs in the plant lineage.
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Abstract
For several decades, only a limited number of noncoding RNAs, such as ribosomal and transfer RNA, have been studied in any depth. In recent years, additional species of noncoding RNAs have increasingly been discovered. Of these, small RNA species attract particular interest because of their essential roles in processes such as RNA silencing and modifications. Detailed analyses revealed several pathways associated with the function of small RNAs. Although these pathways show evolutional conservation, there are substantial differences. Advanced technologies to profile RNAs have accelerated the field further resulting in the discovery of an increasing number of novel species, suggesting that we are only just beginning to appreciate the complexity of small RNAs and their functions. Here, we review recent progress in novel small RNA exploration, including discovered small RNA species, their pathways, and devised technologies.
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Abstract
The nucleolus is a multifunctional compartment of the eukaryotic nucleus. Besides its well-recognised role in transcription and processing of ribosomal RNA and the assembly of ribosomal subunits, the nucleolus has functions in the processing and assembly of a variety of RNPs and is involved in cell cycle control and senescence and as a sensor of stress. Historically, nucleoli have been tenuously linked to the biogenesis and, in particular, export of mRNAs in yeast and mammalian cells. Recently, data from plants have extended the functions in which the plant nucleolus is involved to include transcriptional gene silencing as well as mRNA surveillance and nonsense-mediated decay, and mRNA export. The nucleolus in plants may therefore have important roles in the biogenesis and quality control of mRNAs.
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Affiliation(s)
- Anireddy S. N. Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523 USA
| | - Maxim Golovkin
- Department of Microbiology, Thomas Jefferson University, Philadelphia, PA 19107 USA
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31
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snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene 2007; 408:172-9. [PMID: 18160232 DOI: 10.1016/j.gene.2007.10.037] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 10/19/2007] [Accepted: 10/24/2007] [Indexed: 01/01/2023]
Abstract
Among thousands of non-protein-coding RNAs which have been found in humans, a significant group represents snoRNA molecules that guide other types of RNAs to specific chemical modifications, cleavages, or proper folding. Yet, hundreds of mammalian snoRNAs have unknown function and are referred to as "orphan" molecules. In 2006, for the first time, it was shown that a particular orphan snoRNA (HBII-52) plays an important role in the regulation of alternative splicing of the serotonin receptor gene in humans and other mammals. In order to facilitate the investigation of possible involvement of snoRNAs in the regulation of pre-mRNA processing, we developed a new computational web resource, snoTARGET, which searches for possible guiding sites for snoRNAs among the entire set of human and rodent exonic and intronic sequences. Application of snoTARGET for finding possible guiding sites for a number of human and rodent orphan C/D-box snoRNAs showed that another subgroup of these molecules (HBII-85) have statistically elevated guiding preferences toward exons compared to introns. Moreover, these energetically favorable putative targets of HBII-85 snoRNAs are non-randomly associated with genes producing alternatively spliced mRNA isoforms. The snoTARGET resource is freely available at: (http://hsc.utoledo.edu/depts/bioinfo/snotarget.html).
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Abstract
The family of box H/ACA snoRNA is an abundant class of non-protein-coding RNAs, which play important roles in the post-transcriptional modification of rRNAs and snRNAs. Here we report the characterization in the human genome of 202 sequences derived from box H/ACA snoRNAs. Most of them were retrogenes formed using the L1 integration machinery. About 96% of the box H/ACA RNA-related sequences are found in corresponding locations on the chimpanzee and human chromosomes, while the mouse shares approximately 50% of these human sequences, suggesting that some of the H/ACA RNA-related sequences in primate occurred after the rodent/primate divergence. Of the H/ACA RNA-related sequences, 49% are found in intronic regions of protein-coding genes and 64 H/ACA-related sequences can be folded to the typical secondary structure of the box H/ACA snoRNA family, while 30 of them were recognized as functional homologs of their corresponding box H/ACA snoRNAs previously reported. Of the 64 sequences with the typical secondary structure of the box H/ACA RNA family, 11 were found in EST databases and 5 among which were shown to be expressed in more than one human tissue. Notably, U107f is nested in an intron of a protein gene coding for nudix-type motif 13, but expressed from the opposite strand, and the searching of EST databases revealed it can be expressed in liver and spleen, even in melanotic melanoma.
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Mengel-Jørgensen J, Jensen SS, Rasmussen A, Poehlsgaard J, Iversen JJL, Kirpekar F. Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact. J Biol Chem 2006; 281:22108-22117. [PMID: 16731530 DOI: 10.1074/jbc.m600377200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of eleven modified nucleotides was found in 23 S rRNA, of which eight were singly methylated nucleotides and three were pseudouridines. These modified nucleotides were mapped into the published three-dimensional ribosome structure. Seven of the modified nucleotides located to domain IV, and four modified nucleotides located to domain V of the 23 S rRNA. All posttranscriptionally modified nucleotides map in the center of the ribosome, and none of them are in contact with ribosomal proteins. All except one of the modified nucleotides were found in secondary structure elements of the 23 S ribosomal RNA that contact either 16 S ribosomal RNA or transfer RNA, with five of these nucleotides physically involved in intermolecular RNA-RNA bridges. These findings strongly suggest that the post-transcriptional modifications play a role in modulating intermolecular RNA-RNA contacts, which is the first suggestion on a specific function of endogenous ribosomal RNA modifications.
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Affiliation(s)
- Jonas Mengel-Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Søren Skov Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Anette Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jacob Poehlsgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jens Jørgen Lønsmann Iversen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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Schoemaker RJW, Gultyaev AP. Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding. Nucleic Acids Res 2006; 34:2015-26. [PMID: 16614451 PMCID: PMC1435978 DOI: 10.1093/nar/gkl154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2005] [Revised: 03/12/2006] [Accepted: 03/20/2006] [Indexed: 12/04/2022] Open
Abstract
Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2'-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNA-RNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using computer simulations of rRNA secondary structure formation by genetic algorithm. The effects of sRNA binding on rRNA structure are introduced as temporary structural constraints during co-transcriptional folding. Comparisons of the final predictions with simulations without sRNA binding and with phylogenetic structures show that sRNAs with two antisense elements may significantly facilitate the correct formation of long-range interactions in rRNAs, in particular at elevated temperatures. The simulations suggest that the main mechanism of this effect is a transient restriction of folding in rRNA domains where the termini are brought together by binding to double-guide sRNAs.
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MESH Headings
- Archaeoglobus fulgidus/genetics
- Base Sequence
- Binding Sites
- Computer Simulation
- Molecular Chaperones/chemistry
- Molecular Chaperones/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Pyrococcus abyssi/genetics
- RNA, Antisense/chemistry
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/metabolism
- Temperature
- RNA, Small Untranslated
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Affiliation(s)
- Ruud J. W. Schoemaker
- Section Theoretical Biology, Leiden Institute of Biology, Leiden UniversityKaiserstraat 63, 2311 GP Leiden, The Netherlands
| | - Alexander P. Gultyaev
- Section Theoretical Biology, Leiden Institute of Biology, Leiden UniversityKaiserstraat 63, 2311 GP Leiden, The Netherlands
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35
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Tang TH, Polacek N, Zywicki M, Huber H, Brugger K, Garrett R, Bachellerie JP, Hüttenhofer A. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol Microbiol 2005; 55:469-81. [PMID: 15659164 DOI: 10.1111/j.1365-2958.2004.04428.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
By generating a specialized cDNA library from the archaeon Sulfolobus solfataricus, we have identified 57 novel small non-coding RNA (ncRNA) candidates and confirmed their expression by Northern blot analysis. The majority was found to belong to one of two classes, either antisense or antisense-box RNAs, where the latter only exhibit partial complementarity to RNA targets. The most prominent group of antisense RNAs is transcribed in the opposite orientation to the transposase genes, encoded by insertion elements (transposons). Thus, these antisense RNAs may regulate transposition of insertion elements by inhibiting expression of the transposase mRNA. Surprisingly, the class of antisense RNAs also contained RNAs complementary to tRNAs or sRNAs (small-nucleolar-like RNAs). For the antisense-box ncRNAs, the majority could be assigned to the class of C/D sRNAs, which specify 2'-O-methylation sites on rRNAs or tRNAs. Five C/D sRNAs of this group are predicted to target methylation at six sites in 13 different tRNAs, thus pointing to the widespread role of these sRNA species in tRNA modification in Archaea. Another group of antisense-box RNAs, lacking typical C/D sRNA motifs, was predicted to target the 3'-untranslated regions of certain mRNAs. Furthermore, one of the ncRNAs that does not show antisense elements is transcribed from a repeat unit of a cluster of small regularly spaced repeats in S. solfataricus which is potentially involved in replicon partitioning. In conclusion, this is the first report of stably expressed antisense RNAs in an archaeal species and it raises the prospect that antisense-based mechanisms are also used widely in Archaea to regulate gene expression.
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Affiliation(s)
- Thean-Hock Tang
- Institute for Research in Molecular Medicine, University Sains Malaysia Health Campus, 16150 Kubang Kerian, Kelatan, Malaysia
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36
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Mechanisms and functions of RNA-guided RNA modification. FINE-TUNING OF RNA FUNCTIONS BY MODIFICATION AND EDITING 2004. [DOI: 10.1007/b105585] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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37
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Luo Y, Zhuo H, Li S, Qu L. Identification and functional analysis of a novel box C/D snoRNA fromSchizosaccharomyces pombe. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf03184284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Russell AG, Schnare MN, Gray MW. Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA (NEW YORK, N.Y.) 2004; 10:1034-46. [PMID: 15208440 PMCID: PMC1370595 DOI: 10.1261/rna.7300804] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In eukaryotes, box H/ACA small nucleolar RNAs (snoRNAs) guide sites of pseudouridine (Psi) formation in rRNA. These snoRNAs reside in RNP complexes containing the putative Psi synthase, Cbf5p. In this study we have identified Cbf5p-associated RNAs in Euglena gracilis, an early diverging eukaryote, by immunoprecipitating Cbf5p-containing complexes from cellular extracts. We characterized one box H/ACA-like RNA which, however, does not appear to guide Psi formation in rRNA. We also identified four single Psi-guide box AGA RNAs. We determined target sites for these putative Psi-guide RNAs and confirmed that the predicted Psi modifications do, in fact, occur at these positions in Euglena rRNA. The Cbf5p-associated snoRNAs appear to be encoded by multicopy genes, some of which are clustered in the genome together with methylation-guide snoRNA genes. These modification-guide snoRNAs and snoRNA genes are the first ones to be reported in euglenid protists, the evolutionary sister group to the kinetoplastid protozoa. Unexpectedly, we also found and have partially characterized a selenocysteine tRNA homolog in the anti-Cbf5p-immunoprecipitated sample.
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Affiliation(s)
- Anthony G Russell
- Department of Biochemistry and Molecular Biology, Sir Charles Tupper Medical Building, Room 8F-2, Dal-housie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
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39
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Bortolin ML, Bachellerie JP, Clouet-d'Orval B. In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp). Nucleic Acids Res 2004; 31:6524-35. [PMID: 14602911 PMCID: PMC275556 DOI: 10.1093/nar/gkg860] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Among the large family of C/D methylation guide RNAs, the intron of euryarchaeal pre-tRNA(Trp) represents an outstanding specimen able to guide in cis, instead of in trans, two 2'-O-methylations in the pre-tRNA exons. Remarkably, both sites of methylation involve nucleotides within the bulge-helix-bulge (BHB) splicing motif, while the RNA-guided methylation and pre-tRNA splicing events depend on mutually exclusive RNA folding patterns. Using the three recombinant core proteins of archaeal C/D RNPs, we have analyzed in vitro RNP assembly of the pre-tRNA and tested its site-specific methylation activity. Recognition by L7Ae of hallmark K-turns at the C/D and C'/D' motifs appears as a crucial assembly step required for subsequent binding of a Nop5p-aFib heterodimer at each site. Unexpectedly, however, even without L7Ae but at a higher concentration of Nop5p-aFib, a substantially active RNP complex can still form, possibly reflecting the higher propensity of the cis-acting system to form guide RNA duplex(es) relative to classical trans- acting C/D RNA guides. Moreover, footprinting data of RNPs, consistent with Nop5p interacting with the non-canonical stem of the K-turn, suggest that binding of Nop5p-aFib to the pre-tRNA-L7Ae complex might direct transition from a splicing-competent structure to an RNA conformer displaying the guide RNA duplexes required for site-specific methylation.
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Affiliation(s)
- Marie-Line Bortolin
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099 du CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
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40
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Vitali P, Royo H, Seitz H, Bachellerie JP, Hüttenhofer A, Cavaillé J. Identification of 13 novel human modification guide RNAs. Nucleic Acids Res 2004; 31:6543-51. [PMID: 14602913 PMCID: PMC275545 DOI: 10.1093/nar/gkg849] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Members of the two expanding RNA subclasses termed C/D and H/ACA RNAs guide the 2'-O-methylations and pseudouridylations, respectively, of rRNA and spliceosomal RNAs (snRNAs). Here, we report on the identification of 13 novel human intron-encoded small RNAs (U94-U106) belonging to the two subclasses of modification guides. Seven of them are predicted to direct 2'-O-methylations in rRNA or snRNAs, while the remainder represent novel orphan RNA modification guides. From these, U100, which is exclusively detected in Cajal bodies (CBs), is predicted to direct modification of a U6 snRNA uridine, U(9), which to date has not been found to be pseudouridylated. Hence, within CBs, U100 might function in the folding pathway or other aspects of U6 snRNA metabolism rather than acting as a pseudouridylation guide. U106 C/D snoRNA might also possess an RNA chaperone activity only since its two conserved antisense elements match two rRNA sequences devoid of methylated nucleotides and located remarkably close to each other within the 18S rRNA secondary structure. Finally, we have identified a retrogene for U99 snoRNA located within an intron of the Siat5 gene, supporting the notion that retro-transposition events might have played a substantial role in the mobility and diversification of snoRNA genes during evolution.
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Affiliation(s)
- Patrice Vitali
- Institute for Molecular Biology, Department of Functional Genomics, University of Innsbruck, Peter-Mayr-Strasse 4b, 6020 Innsbruck, Austria
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41
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Massardo DR, Esposito B, Veneziano A, Wolf K, Alifano P, Del Giudice L. Hyper-expression of small nucleolar RNAs (snoRNAs) in female inflorescences of hazelnut (Corylus avellana L.) supports rRNA aggregation in vitro. PLANT & CELL PHYSIOLOGY 2003; 44:884-892. [PMID: 14519769 DOI: 10.1093/pcp/pcg111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Under certain in vitro (salt and temperature) conditions rRNA aggregation occurs in female inflorescences but not in leaves or pollen RNA preparations from hazelnut (Corylus avellana L.), a species of economic interest. This paper describes experiments addressing an explanation of this phenomenon. The experiments demonstrate that: (i) trans-acting factors induce rRNA aggregate formation in female inflorescences RNA preparations; (ii) these factors support aggregation also of heterologous rRNA; (iii) aggregation is a function of temperature pre-treatment of rRNA and not of source 18S rRNA; (iv) the factors inducing rRNA aggregates are sensitive to RNase; (v) antisense small nucleolar RNAs (snoRNAs) participate in rRNA aggregate formation. snoRNAs are involved in pre-rRNA spacer cleavages, and are required for the two most common types of rRNA modifications: 2'-O-ribose methylation and pseudouridylation. Even though it is questionable whether rRNA aggregation really happens in female inflorescence in vivo, the phenomenon observed in vitro may reflect the abundance of snoRNAs in these reproductive structures. In fact the level of accumulation of three tested snoRNAs, R1, U14 and U3, is much higher in female inflorescence than in leaves or pollen of hazelnut. This finding opens the possibility of studying the role of snoRNAs in tissue development in plants.
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Affiliation(s)
- Domenica Rita Massardo
- Istituto di Genetica e Biofisica Adriano Buzzati-Traverso--C.N.R., Via G. Marconi 10, I-80125 Napoli, Italy
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42
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Abstract
Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal RNA (pre-rRNA) processing and rRNA base modifications (2'-O-ribose methylation and pseudouridylation). Their genomic organization show great flexibility: some are individually or polycistronically transcribed, while others are encoded within introns of other genes. Here, we present an evolutionary analysis of the U49 gene in seven species. In all species analyzed, U49 contains the typical hallmarks of C and D box motifs, and a conserved 12-15 nt sequence complementary to rRNA that define them as homologs. In mouse, human, and Drosophila U49 is found encoded within introns of different genes, and in plants it is transcribed polycistronically from four different locations. In addition, U49 has two copies in two different introns of the RpL14 gene in Drosophila. The results indicate a substantial degree of duplication and translocation of the U49 gene in evolution. In light of its variable organization we discuss which of the two proposed mechanisms of rearrangement has acted upon the U49 snoRNA gene: chromosomal duplication or transposition through an RNA intermediate.
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Affiliation(s)
- Espen Enerly
- Division of Molecular Biology, Institute of Biology, University of Oslo, Blindern, Oslo, Norway
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43
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Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH. The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res 2003; 31:2601-13. [PMID: 12736310 PMCID: PMC156054 DOI: 10.1093/nar/gkg373] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Revised: 02/18/2003] [Accepted: 03/25/2003] [Indexed: 11/14/2022] Open
Abstract
Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2'-O-ribose methylation sites in rice rRNAs. Though not exhaustive, this analysis has revealed that rice has the highest number of known box C/D snoRNAs among eukaryotes. Interestingly, although many snoRNA genes are conserved between rice and Arabidopsis, almost half of the identified snoRNA genes are rice specific, which may highlight further the differences in rRNA methylation patterns between monocotyledons and dicotyledons. In addition to 76 singletons, 70 clusters involving 270 snoRNA genes were also found in rice. The large number of the novel snoRNA polycistrons found in the introns of rice protein-coding genes is in contrast to the one-snoRNA-per-intron organization of vertebrates and yeast, and of Arabidopsis in which only a few intronic snoRNA gene clusters were identified. Furthermore, due to a high degree of gene duplication, rice snoRNA genes are clearly redundant and exhibit great sequence variation among isoforms, allowing generation of new snoRNAs for selection. Thus, the large snoRNA gene family in plants can serve as an excellent model for a rapid and functional evolution.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Gene Library
- Genes, Plant/genetics
- Genetic Variation
- Genome, Plant
- Methylation
- Molecular Sequence Data
- Multigene Family/genetics
- Oryza/genetics
- Plants/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribose/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Chun-Long Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhoushan University, Guangzhou 510275, China
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44
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Kruszka K, Barneche F, Guyot R, Ailhas J, Meneau I, Schiffer S, Marchfelder A, Echeverría M. Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J 2003; 22:621-32. [PMID: 12554662 PMCID: PMC140725 DOI: 10.1093/emboj/cdg040] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) guiding modifications of ribosomal RNAs and other RNAs display diverse modes of gene organization and expression depending on the eukaryotic system: in animals most are intron encoded, in yeast many are monocistronic genes and in plants most are polycistronic (independent or intronic) genes. Here we report an unprecedented organization: plant dicistronic tRNA-snoRNA genes. In Arabidopsis thaliana we identified a gene family encoding 12 novel box C/D snoRNAs (snoR43) located just downstream from tRNA(Gly) genes. We confirmed that they are transcribed, probably from the tRNA gene promoter, producing dicistronic tRNA(Gly)-snoR43 precursors. Using transgenic lines expressing a tagged tRNA-snoR43.1 gene we show that the dicistronic precursor is accurately processed to both snoR43.1 and tRNA(Gly). In addition, we show that a recombinant RNase Z, the plant tRNA 3' processing enzyme, efficiently cleaves the dicistronic precursor in vitro releasing the snoR43.1 from the tRNA(Gly). Finally, we describe a similar case in rice implicating a tRNA(Met-e) expressed in fusion with a novel C/D snoRNA, showing that this mode of snoRNA expression is found in distant plant species.
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Affiliation(s)
| | - Fredy Barneche
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Romain Guyot
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | | | | | - Steffen Schiffer
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Anita Marchfelder
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Manuel Echeverría
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
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45
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Brown JWS, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Hüttenhofer A, Kastenmayer JP, Green PJ, Shaw P, Marshall DF. Plant snoRNA database. Nucleic Acids Res 2003; 31:432-5. [PMID: 12520043 PMCID: PMC165456 DOI: 10.1093/nar/gkg009] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Plant snoRNA database (http://www.scri.sari.ac.uk/plant_snoRNA/) provides information on small nucleolar RNAs from Arabidopsis and eighteen other plant species. Information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. The Arabidopsis information is divided into box C/D and box H/ACA snoRNAs, and within each of these groups, by target sites in rRNA, snRNA or unknown. Alignments of orthologous genes and gene variants from different plant species are available for many snoRNA genes. Plant snoRNA genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.
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Affiliation(s)
- John W S Brown
- Gene Expression Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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46
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Brown JWS, Echeverria M, Qu LH. Plant snoRNAs: functional evolution and new modes of gene expression. TRENDS IN PLANT SCIENCE 2003; 8:42-9. [PMID: 12523999 DOI: 10.1016/s1360-1385(02)00007-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are a well-characterized family of non-coding RNAs whose main function is rRNA modification. The diversity and complexity of this gene family continues to expand with the discovery of snoRNAs with non-rRNA or unknown targets. Plants contain more snoRNAs than other eukaryotes and have developed novel expression and processing strategies. The increased number of modifications, which will influence ribosome function, and the novel modes of expression might reflect the environmental conditions to which plants are exposed. Polyploidy and chromosomal rearrangements have generated multiple copies of snoRNA genes, allowing the generation of new snoRNAs for selection. The large snoRNA family in plants is an ideal model for investigation of mechanisms of evolution of gene families in plants.
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MESH Headings
- Base Sequence
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Plants/genetics
- Plants/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/physiology
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- John W S Brown
- Gene Expression Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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47
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Marker C, Zemann A, Terhörst T, Kiefmann M, Kastenmayer JP, Green P, Bachellerie JP, Brosius J, Hüttenhofer A. Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr Biol 2002; 12:2002-13. [PMID: 12477388 DOI: 10.1016/s0960-9822(02)01304-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Genomes from all organisms known to date express two types of RNA molecules: messenger RNAs (mRNAs), which are translated into proteins, and non-messenger RNAs, which function at the RNA level and do not serve as templates for translation. RESULTS We have generated a specialized cDNA library from Arabidopsis thaliana to investigate the population of small non-messenger RNAs (snmRNAs) sized 50-500 nt in a plant. From this library, we identified 140 candidates for novel snmRNAs and investigated their expression, abundance, and developmental regulation. Based on conserved sequence and structure motifs, 104 snmRNA species can be assigned to novel members of known classes of RNAs (designated Class I snmRNAs), namely, small nucleolar RNAs (snoRNAs), 7SL RNA, U snRNAs, as well as a tRNA-like RNA. For the first time, 39 novel members of H/ACA box snoRNAs could be identified in a plant species. Of the remaining 36 snmRNA candidates (designated Class II snmRNAs), no sequence or structure motifs were present that would enable an assignment to a known class of RNAs. These RNAs were classified based on their location on the A. thaliana genome. From these, 29 snmRNA species located to intergenic regions, 3 located to intronic sequences of protein coding genes, and 4 snmRNA candidates were derived from annotated open reading frames. Surprisingly, 15 of the Class II snmRNA candidates were shown to be tissue-specifically expressed, while 12 are encoded by the mitochondrial or chloroplast genome. CONCLUSIONS Our study has identified 140 novel candidates for small non-messenger RNA species in the plant A. thaliana and thereby sets the stage for their functional analysis.
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Affiliation(s)
- Claudia Marker
- Institute of Experimental Pathology, ZMBE, Von-Esmarch-Str 56, 48149 Münster, Germany
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48
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Hüttenhofer A, Brosius J, Bachellerie JP. RNomics: identification and function of small, non-messenger RNAs. Curr Opin Chem Biol 2002; 6:835-43. [PMID: 12470739 DOI: 10.1016/s1367-5931(02)00397-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In the past few years, our knowledge about small non-mRNAs (snmRNAs) has grown exponentially. Approaches including computational and experimental RNomics have led to a plethora of novel snmRNAs, especially small nucleolar RNAs (snoRNAs). Members of this RNA class guide modification of ribosomal and spliceosomal RNAs. Novel targets for snoRNAs were identified such as tRNAs and potentially mRNAs, and several snoRNAs were shown to be tissue-specifically expressed. In addition, previously unknown classes of snmRNAs have been discovered. MicroRNAs and small interfering RNAs of about 21-23 nt, were shown to regulate gene expression by binding to mRNAs via antisense elements. Regulation of gene expression is exerted by degradation of mRNAs or translational regulation. snmRNAs play a variety of roles during regulation of gene expression. Moreover, the function of some snmRNAs known for decades, has been finally elucidated. Many other RNAs were identified by RNomics studies lacking known sequence and structure motifs. Future challenges in the field of RNomics include identification of the novel snmRNA's biological roles in the cell.
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Affiliation(s)
- Alexander Hüttenhofer
- Institute of Experimental Pathology, ZMBE, Von-Esmarch-Str. 56, 48149, Münster, Germany.
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49
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Abstract
In eukaryotes, the site-specific formation of the two prevalent types of rRNA modified nucleotides, 2'-O-methylated nucleotides and pseudouridines, is directed by two large families of snoRNAs. These are termed box C/D and H/ACA snoRNAs, respectively, and exert their function through the formation of a canonical guide RNA duplex at the modification site. In each family, one snoRNA acts as a guide for one, or at most two modifications, through a single, or a pair of appropriate antisense elements. The two guide families now appear much larger than anticipated and their role not restricted to ribosome synthesis only. This is reflected by the recent detection of guides that can target other cellular RNAs, including snRNAs, tRNAs and possibly even mRNAs, and by the identification of scores of tissue-specific specimens in mammals. Recent characterization of homologs of eukaryotic modification guide snoRNAs in Archaea reveals the ancient origin of these non-coding RNA families and offers new perspectives as to their range of function.
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Affiliation(s)
- Jean Pierre Bachellerie
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, Université Paul-Sabatier, 118, route de Narbonne, 31062 Toulouse cedex 4,France.
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50
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Liang D, Zhou H, Zhang P, Chen YQ, Chen X, Chen CL, Qu LH. A novel gene organization: intronic snoRNA gene clusters from Oryza sativa. Nucleic Acids Res 2002; 30:3262-72. [PMID: 12136108 PMCID: PMC135747 DOI: 10.1093/nar/gkf426] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Based on the analysis of structural features and conserved elements, 27 novel snoRNA genes have been identified from rice. All of them belong to the C/D box-containing snoRNA family except for one that belongs to the H/ACA box type. The newly found genes fall into six clusters that comprise at least three snoRNA genes, and in one case as many as nine genes. Interestingly, four of the six clusters are located within the largest intron of a protein coding gene. The majority of intronic snoRNA gene clusters are simply formed by multiple copies of the same species of snoRNA gene that possess the identical functional elements. This implies a possible mechanism of duplication for the origin of repeating snoRNA coding regions in one intron. However, a few intronic snoRNA gene clusters consisting of different snoRNAs species were also observed. Polycistronic precursors from two independently transcribed clusters were demonstrated by RT-PCR and individual snoRNAs processed from the polycistronic precursors were positively determined by reverse transcription assay. Analyses of the intergenic spacers in the clusters showed that, in addition to a very high AT content, the processing signals in rice snoRNA polycistronic transcripts might be different from those of yeast. Our results demonstrate that, in both plants and mammals, numerous snoRNAs can be produced simultaneously from an mRNA precursor of a host gene despite the different arrangements. The intronic snoRNA gene cluster is a novel gene organization, which is so far unique to plants. The conservation of intronic snoRNA gene clusters in plants was further demonstrated by the study of a similar snoRNA gene organization in the first intron of a Hsp70 gene from wild rice and Zizania caduciflora.
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Affiliation(s)
- Dan Liang
- Key Laboratory of Gene Engineering of Education Ministry, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, People's Republic of China
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