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Wang J, Wu S, Ye K. Complicated target recognition by archaeal box C/D guide RNAs. SCIENCE CHINA. LIFE SCIENCES 2024; 67:631-644. [PMID: 38041781 DOI: 10.1007/s11427-022-2412-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 12/03/2023]
Abstract
Box C/D RNAs guide the site-specific formation of 2'-O-methylated nucleotides (Nm) of RNAs in eukaryotes and archaea. Although C/D RNAs have been profiled in several archaea, their targets have not been experimentally determined. Here, we mapped Nm in rRNAs, tRNAs, and abundant small RNAs (sRNAs) and profiled C/D RNAs in the crenarchaeon Sulfolobus islandicus. The targets of C/D RNAs were assigned by analysis of base-pairing interactions, in vitro modification assays, and gene deletion experiments, revealing a complicated landscape of C/D RNA-target interactions. C/D RNAs widely use dual antisense elements to target adjacent sites in rRNAs, enhancing modification at weakly bound sites. Two consecutive sites can be guided with the same antisense element upstream of box D or D', a phenomenon known as double-specificity that is exclusive to internal box D' in eukaryotic C/D RNAs. Several C/D RNAs guide modification at a single non-canonical site. This study reveals the global landscape of RNA-guided 2'-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.
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Affiliation(s)
- Jiayin Wang
- Key Laboratory of RNA Science and Engineering, 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 Science and Engineering, 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
| | - Keqiong Ye
- Key Laboratory of RNA Science and Engineering, 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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2
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Benrezkallah D. Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway. J Mol Graph Model 2024; 127:108700. [PMID: 38183846 DOI: 10.1016/j.jmgm.2023.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Most life forms on earth live at temperatures below 50 °C. Within these organisms are proteins that form the three-dimensional structures essential to their biological activity and function. However, some thermophilic life forms can resist higher temperatures and have corresponding adaptations to preserve protein function at these high temperatures. Among the structural factors responsible for this resistance of thermophilic proteins to high temperatures is the presence of additional hydrogen bonds in the thermophilic proteins, which means that the structure of the protein is more resistant to unfolding. Similarly, thermostable proteins are rich in structure-stabilizing salt bridges and/or disulfide bridges. In this context, we perform multiple replica molecular dynamics simulations at different temperatures on the Aeropyrum pernix (L7Ae) protein (from the crenarchaeal species A. pernix), known for its high melting temperature, and this in the aim to elucidate the structural factors responsible for its high thermostability. The results reveal that between the most sensitive regions of the protein to the increase of temperature are the loops L1, and L5, which surround the hydrophobic core region of the protein, besides the loop L9, and the C-terminal α5 region. This latter is the longer alpha helix of the protein secondary structure motifs and it is the first to be denaturated at 450 K, while the rest of the protein secondary structure motifs at this temperature were intact. The mechanism of unfolding that follows this protein at 550 K is similar to other thermophile proteins found in literature, with the opening of the loops that surround the hydrophobic core of the protein. So, the latter is completely exposed to the solvent, and partially denatured. The total denaturation process of the protein takes an average time of 40 ns to be achieved. Our investigation also shows that all the calculated salt bridges, with distances less than or equal to 6 A°, are on the periphery part of the protein, exposed to the solvent. However, the hydrophobic core of the protein is not involved in the formation of salt bridges, but rather with formation of some important hydrogen bondings that still persist even at 450 K. So, optimizing hydrogen bonding, near or within the core region, at high temperatures is a strategy that follows this thermostable protein to protect its hydrophobic core from denaturation, and ensure the thermal stability of the protein.
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Affiliation(s)
- Djamila Benrezkallah
- Department of Basic Teachings in Sciences and Technologies (EBST), Faculty of Technology, Djillali Liabes University, Ben M'Hidi BP 89, Sidi Bel Abbes 22000, Algeria; LCPM Laboratory, Chemistry Department, Faculty of Exact and Applied Sciences, University Oran 1 Ahmed Ben Bella, El Mnaouer BP 1524, Oran 31000, Algeria.
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3
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Mu Y, Han J, Wu M, Li Z, DU K, Wei Y, Wu M, Huang J. Fibrillarin promotes homologous recombination repair by facilitating the recruitment of recombinase RAD51 to DNA damage sites. J Zhejiang Univ Sci B 2023; 24:1165-1173. [PMID: 38057273 PMCID: PMC10710916 DOI: 10.1631/jzus.b2300518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/10/2023] [Indexed: 12/08/2023]
Abstract
Eukaryotic organisms constantly face a wide range of internal and external factors that cause damage to their DNA. Failure to accurately and efficiently repair these DNA lesions can result in genomic instability and the development of tumors (Canela et al., 2017). Among the various forms of DNA damage, DNA double-strand breaks (DSBs) are particularly harmful. Two major pathways, non-homologous end joining (NHEJ) and homologous recombination (HR), are primarily responsible for repairing DSBs (Katsuki et al., 2020; Li and Yuan, 2021; Zhang and Gong, 2021; Xiang et al., 2023). NHEJ is an error-prone repair mechanism that simply joins the broken ends together (Blunt et al., 1995; Hartley et al., 1995). In contrast, HR is a precise repair process. It involves multiple proteins in eukaryotic cells, with the RAD51 recombinase being the key player, which is analogous to bacterial recombinase A (RecA) (Shinohara et al., 1992). The central event in HR is the formation of RAD51-single-stranded DNA (ssDNA) nucleoprotein filaments that facilitate homology search and DNA strand invasion, ultimately leading to the initiation of repair synthesis (Miné et al., 2007; Hilario et al., 2009; Ma et al., 2017).
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Affiliation(s)
- Yanhua Mu
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jinhua Han
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310030, China
| | - Mingjie Wu
- Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Zongfang Li
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Ke DU
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Yameng Wei
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Mengjie Wu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China. ,
| | - Jun Huang
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310030, China.
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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Abstract
Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, N6-methyladenosine (m6A). We first describe the discovery of the key enzymes that deposit and remove m6A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m6A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
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Zhao S, Zhang D, Liu S, Huang J. The roles of NOP56 in cancer and SCA36. Pathol Oncol Res 2023; 29:1610884. [PMID: 36741964 PMCID: PMC9892063 DOI: 10.3389/pore.2023.1610884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023]
Abstract
NOP56 is a highly conserved nucleolar protein. Amplification of the intron GGCCTG hexanucleotide repeat sequence of the NOP56 gene results in spinal cerebellar ataxia type 36 (SCA36). NOP56 contains an N-terminal domain, a coiled-coil domain, and a C-terminal domain. Nucleolar protein NOP56 is significantly abnormally expressed in a number of malignant tumors, and its mechanism is different in different tumors, but its regulatory mechanism in most tumors has not been fully explored. NOP56 promotes tumorigenesis in some cancers and inhibits tumorigenesis in others. In addition, NOP56 is associated with methylation in some tumors, suggesting that NOP56 has the potential to become a tumor-specific marker. This review focuses on the structure, function, related signaling pathways, and role of NOP56 in the progression of various malignancies, and discusses the progression of NOP56 in neurodegenerative and other diseases.
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Affiliation(s)
- Shimin Zhao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dongdong Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Jun Huang,
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Wang J, Yang Z, Ye K. Methylation guide RNAs without box C/D motifs. RNA (NEW YORK, N.Y.) 2022; 28:1597-1605. [PMID: 36127125 PMCID: PMC9670817 DOI: 10.1261/rna.079379.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The defining feature of methylation guide RNAs is two sets of box C and D motifs that form kink-turn structures specifically recognized by L7Ae family proteins. Here, we engineered a new type of methylation guide that lacks C/D motifs and requires no L7Ae for assembly and function. We determined a crystal structure of a bipartite C/D-free guide RNA in complex with Nop5, fibrillarin and substrate in the active form at 2.2 Å resolution. The stems of new guide RNAs functionally replace C/D motifs in Nop5 binding, precisely placing the substrate for site-specific modification. We also found that the bipartite architecture and association of L7Ae with C/D motifs enhance modification when association of guide RNAs or substrates is weak. Our study provides insights into the variations, robustness and possible evolutionary path of methylation guide RNAs.
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Affiliation(s)
- 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
| | - Zuxiao Yang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang 050017, Hebei, 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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Thalalla Gamage S, Bortolin-Cavaillé ML, Link C, Bryson K, Sas-Chen A, Schwartz S, Cavaillé J, Meier JL. Antisense pairing and SNORD13 structure guide RNA cytidine acetylation. RNA (NEW YORK, N.Y.) 2022; 28:1582-1596. [PMID: 36127124 PMCID: PMC9670809 DOI: 10.1261/rna.079254.122] [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: 05/13/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023]
Abstract
N4-acetylcytidine (ac4C) is an RNA nucleobase found in all domains of life. The establishment of ac4C in helix 45 (h45) of human 18S ribosomal RNA (rRNA) requires the combined activity of the acetyltransferase NAT10 and the box C/D snoRNA SNORD13. However, the molecular mechanisms governing RNA-guided nucleobase acetylation in humans remain unexplored. After applying comparative sequence analysis and site-directed mutagenesis to provide evidence that SNORD13 folds into three main RNA helices, we report two assays that enable the study of SNORD13-dependent RNA acetylation in human cells. First, we demonstrate that ectopic expression of SNORD13 rescues h45 in a SNORD13 knockout cell line. Next, we show that mutant snoRNAs can be used in combination with nucleotide resolution ac4C sequencing to define structure and sequence elements critical for SNORD13 function. Finally, we develop a second method that reports on the substrate specificity of endogenous NAT10-SNORD13 via mutational analysis of an ectopically expressed pre-rRNA substrate. By combining mutational analysis of these reconstituted systems with nucleotide resolution ac4C sequencing, our studies reveal plasticity in the molecular determinants underlying RNA-guided cytidine acetylation that is distinct from deposition of other well-studied rRNA modifications (e.g., pseudouridine). Overall, our studies provide a new approach to reconstitute RNA-guided cytidine acetylation in human cells as well as nucleotide resolution insights into the mechanisms governing this process.
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Affiliation(s)
| | - Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Courtney Link
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Keri Bryson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Aldema Sas-Chen
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6195001 Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jérôme Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
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Keppeke GD, Satoh M, Kayser C, Matos P, Hasegawa T, Tanaka S, Diogenes L, Amaral RQ, Rodrigues S, Andrade LEC. A cell-based assay for detection of anti-fibrillarin autoantibodies with performance equivalent to immunoprecipitation. Front Immunol 2022; 13:1011110. [PMID: 36225928 PMCID: PMC9549361 DOI: 10.3389/fimmu.2022.1011110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Anti-fibrillarin autoantibodies are useful for the diagnosis and prognosis of systemic sclerosis (SSc). Anti-fibrillarin produces a clumpy nucleolar pattern in indirect immunofluorescence assay on HEp-2 cells (HEp-2 IFA). Here we develop and validate a reliable cell-based anti-fibrillarin assay (Fibrillarin/CBA) for use in clinical diagnostic laboratories. A TransMembrane Signal was fused to the human fibrillarin gene (TMS-fibrillarin). HEp-2 cells overexpressing transgenic TMS-fibrillarin at the cytoplasmic membrane were used as IFA substrate in the Fibrillarin/CBA. Sixty-two serum samples with nucleolar pattern in the HEp-2 IFA (41 clumpy; 21 homogeneous/punctate) were tested for anti-fibrillarin using Fibrillarin/CBA, immunoprecipitation (IP), line-blot and ELISA. In addition, samples from 106 SSc-patients were evaluated with Fibrillarin/CBA and the results were correlated with disease phenotypes. Thirty-eight of 41 samples with the clumpy nucleolar pattern (92.7%) were positive in the Fibrillarin/CBA, while all 21 samples with other nucleolar patterns were negative. Fibrillarin/CBA results agreed 100% with IP results. Among the 38 Fibrillarin/CBA-positive samples, only 15 (39.5%) and 11 (29%) were positive for anti-fibrillarin in line-blot and ELISA, respectively. Higher frequency of diffuse cutaneous SSc (dcSSc) phenotype (72.7% vs 36.8%; p=0.022), cardiac involvement (36.4% vs 6.5%; p=0.001) and scleroderma renal crisis (18.2% vs 3.3% p = 0.028) was observed in SSc patients with positive compared to negative Fibrillarin/CBA result. Performance of Fibrillarin/CBA in the detection of anti-fibrillarin autoantibodies was comparable to the gold standard IP. Positive Fibrillarin/CBA results correlated with disease phenotypes known to be associated with anti-fibrillarin autoantibodies, underscoring the clinical validation of this novel assay.
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Affiliation(s)
- Gerson Dierley Keppeke
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, Brazil
- *Correspondence: Gerson Dierley Keppeke,
| | - Minoru Satoh
- Department of Clinical Nursing, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
- Department of Medicine, Kitakyushu Yahata-Higashi Hospital, Kitakyushu, Japan
| | - Cristiane Kayser
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Pedro Matos
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Tomoko Hasegawa
- Department of Clinical Nursing, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Shin Tanaka
- Department of Human, Information, and Science, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Larissa Diogenes
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, Brazil
| | | | - Silvia Helena Rodrigues
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Luis Eduardo Coelho Andrade
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, Brazil
- Immunology Division, Fleury Laboratory, Sao Paulo, Brazil
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Ren X, Zhang H, Yan X, Sun Y, Xu T. NOP56 negatively regulates MyD88-mediated NF-κB signaling in miiuy croaker, Miichthys miiuy. FISH & SHELLFISH IMMUNOLOGY 2022; 120:75-81. [PMID: 34774735 DOI: 10.1016/j.fsi.2021.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
MyD88 is a critical adaptor in the TLRs signaling pathway, which can activate NF-κB signaling pathway and promote proinflammatory cytokines production. However, the molecular mechanisms that modulate MyD88 expression, especially in teleost, remain largely unknown. In this study, we showed that NOP56 serve as a negative regulator of the MyD88-mediated NF-κB signaling pathway. NOP56 overexpression inhibited the protein expression of MyD88. Whereas, siRNA knockdown of NOP56 had opposite effect. Furthermore, we found that the NOSIC domain is responsible for the suppressive effect of NOP56 in MyD88 expression at protein level. Therefore, we identified NOP56 as a negative regulator of MyD88-mediated NF-κB signaling by inhibiting MyD88 expression and provided new insight into the regulation mechanism in teleost fish.
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Affiliation(s)
- Xiaomeng Ren
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Han Zhang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaolong Yan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, China.
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China.
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10
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Shi Y, El-Deeb IM, Masic V, Hartley-Tassell L, Maggioni A, Itzstein MV, Ve T. Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin. Pharmaceuticals (Basel) 2021; 15:26. [PMID: 35056083 PMCID: PMC8779173 DOI: 10.3390/ph15010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
Abstract
Fibrillarin (FBL) is an essential and evolutionarily highly conserved S-adenosyl methionine (SAM) dependent methyltransferase. It is the catalytic component of a multiprotein complex that facilitates 2'-O-methylation of ribosomal RNAs (rRNAs), a modification essential for accurate and efficient protein synthesis in eukaryotic cells. It was recently established that human FBL (hFBL) is critical for Nipah, Hendra, and respiratory syncytial virus infections. In addition, overexpression of hFBL contributes towards tumorgenesis and is associated with poor survival in patients with breast cancer, suggesting that hFBL is a potential target for the development of both antiviral and anticancer drugs. An attractive strategy to target cofactor-dependent enzymes is the selective inhibition of cofactor binding, which has been successful for the development of inhibitors against several protein methyltransferases including PRMT5, DOT1L, and EZH2. In this work, we solved crystal structures of the methyltransferase domain of hFBL in apo form and in complex with the cofactor SAM. Screening of a fluorinated fragment library, via X-ray crystallography and 19F NMR spectroscopy, yielded seven hit compounds that competed with cofactor binding, two of which resulted in co-crystal structures. One of these structures revealed unexpected conformational variability in the cofactor binding site, which allows it to accommodate a compound significantly different from SAM. Our structural data provide critical information for the design of selective cofactor competitive inhibitors targeting hFBL, and preliminary elaboration of hit compounds has led to additional cofactor site binders.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Ibrahim M El-Deeb
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Andrea Maggioni
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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Motorin Y, Quinternet M, Rhalloussi W, Marchand V. Constitutive and variable 2'-O-methylation (Nm) in human ribosomal RNA. RNA Biol 2021; 18:88-97. [PMID: 34503375 PMCID: PMC8677024 DOI: 10.1080/15476286.2021.1974750] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/30/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
Epitranscriptomic modifications of stable RNAs are dynamically regulated and specific profiles of 2'-O-methylation in rRNA have been associated with distinct cancer types. However, these observations pointed out the existence of at least two distinct groups: a rather large group with constitutive rRNA Nm residues exhibiting a stable level of methylation and a more restricted set of variable modifications, giving rise to the concept of 'specialized ribosomes'. These heterogeneous ribosomes can modulate their translational properties and be key regulatory players, depending on the physiological state of the cell. However, these conclusions were drawn from a limited set of explored human cell lines or tissues, mostly related to cancer cells of the same type. Here, we report a comprehensive analysis of human rRNA Nm modification variability observed for >15 human cell lines grown in different media and conditions. Our data demonstrate that human Nm sites can be classified into four groups, depending on their observed variability. About ⅓ of rRNA 2'-O-methylations are almost invariably modified at the same level in all tested samples (stable modifications), the second group of relatively invariant modifications (another ½ of the total) showing a slightly higher variance (low variable group) and two variable groups, showing an important heterogeneity. Mapping of these four classes on the human ribosome 3D structure shows that stably modified positions are preferentially located in the important ribosome functional sites, while variable and highly variable residues are mostly distributed to the ribosome periphery. Possible relationships of such stable and variable modifications to the ribosome functions are discussed.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, F-54000 Nancy, France
| | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, B2S Core Facility, F-54000 Nancy, France
| | - Wassim Rhalloussi
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, F-54000 Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, F-54000 Nancy, France
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12
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Baldini L, Charpentier B, Labialle S. Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs. Noncoding RNA 2021; 7:ncrna7020030. [PMID: 34066559 PMCID: PMC8162545 DOI: 10.3390/ncrna7020030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.
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Affiliation(s)
| | - Bruno Charpentier
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| | - Stéphane Labialle
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
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13
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Breuer R, Gomes-Filho JV, Randau L. Conservation of Archaeal C/D Box sRNA-Guided RNA Modifications. Front Microbiol 2021; 12:654029. [PMID: 33776983 PMCID: PMC7994747 DOI: 10.3389/fmicb.2021.654029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional modifications fulfill many important roles during ribosomal RNA maturation in all three domains of life. Ribose 2'-O-methylations constitute the most abundant chemical rRNA modification and are, for example, involved in RNA folding and stabilization. In archaea, these modification sites are determined by variable sets of C/D box sRNAs that guide the activity of the rRNA 2'-O-methyltransferase fibrillarin. Each C/D box sRNA contains two guide sequences that can act in coordination to bridge rRNA sequences. Here, we will review the landscape of archaeal C/D box sRNA genes and their target sites. One focus is placed on the apparent accelerated evolution of guide sequences and the varied pairing of the two individual guides, which results in different rRNA modification patterns and RNA chaperone activities.
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Affiliation(s)
| | | | - Lennart Randau
- Prokaryotic RNA Biology, Philipps-Universität Marburg, Marburg, Germany
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14
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Yang Z, Wang J, Huang L, Lilley DMJ, Ye K. Functional organization of box C/D RNA-guided RNA methyltransferase. Nucleic Acids Res 2020; 48:5094-5105. [PMID: 32297938 PMCID: PMC7229835 DOI: 10.1093/nar/gkaa247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/14/2022] Open
Abstract
Box C/D RNA protein complexes (RNPs) catalyze site-specific 2'-O-methylation of RNA with specificity determined by guide RNAs. In eukaryotic C/D RNP, the paralogous Nop58 and Nop56 proteins specifically associate with terminal C/D and internal C'/D' motifs of guide RNAs, respectively. We have reconstituted active C/D RNPs with recombinant proteins of the thermophilic yeast Chaetomium thermophilum. Nop58 and Nop56 could not distinguish between the two C/D motifs in the reconstituted enzyme, suggesting that the assembly specificity is imposed by trans-acting factors in vivo. The two C/D motifs are functionally independent and halfmer C/D RNAs can also guide site-specific methylation. Extensive pairing between C/D RNA and substrate is inhibitory to modification for both yeast and archaeal C/D RNPs. N6-methylated adenine at box D/D' interferes with the function of the coupled guide. Our data show that all C/D RNPs share the same functional organization and mechanism of action and provide insight into the assembly specificity of eukaryotic C/D RNPs.
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Affiliation(s)
- Zuxiao Yang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang 050017, Hebei, 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
| | - Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - 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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15
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Phung DK, Etienne C, Batista M, Langendijk-Genevaux P, Moalic Y, Laurent S, Liuu S, Morales V, Jebbar M, Fichant G, Bouvier M, Flament D, Clouet-d’Orval B. RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery. Nucleic Acids Res 2020; 48:3832-3847. [PMID: 32030412 PMCID: PMC7144898 DOI: 10.1093/nar/gkaa052] [Citation(s) in RCA: 9] [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: 10/24/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 01/22/2023] Open
Abstract
A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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Affiliation(s)
- Duy Khanh Phung
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Clarisse Etienne
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Petra Langendijk-Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Yann Moalic
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sophie Liuu
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Violette Morales
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Mohamed Jebbar
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Didier Flament
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Béatrice Clouet-d’Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
- To whom correspondence should be addressed. Tel: +33 561 335 875; Fax: +33 561 335 886;
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16
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Khoshnevis S, Dreggors RE, Hoffmann TFR, Ghalei H. A conserved Bcd1 interaction essential for box C/D snoRNP biogenesis. J Biol Chem 2019; 294:18360-18371. [PMID: 31537647 DOI: 10.1074/jbc.ra119.010222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Precise modification and processing of rRNAs are required for the production of ribosomes and accurate translation of proteins. Small nucleolar ribonucleoproteins (snoRNPs) guide the folding, modification, and processing of rRNAs and are thus critical for all eukaryotic cells. Bcd1, an essential zinc finger HIT protein functionally conserved in eukaryotes, has been implicated as an early regulator for biogenesis of box C/D snoRNPs and controls steady-state levels of box C/D snoRNAs through an unknown mechanism. Using a combination of genetic and biochemical approaches, here we found a conserved N-terminal motif in Bcd1 from Saccharomyces cerevisiae that is required for interactions with box C/D snoRNAs and the core snoRNP protein, Snu13. We show that both the Bcd1-snoRNA and Bcd1-Snu13 interactions are critical for snoRNP assembly and ribosome biogenesis. Our results provide mechanistic insight into Bcd1 interactions that likely control the early steps of snoRNP maturation and contribute to the essential role of this protein in maintaining the steady-state levels of snoRNAs in the cell.
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Affiliation(s)
- Sohail Khoshnevis
- Department of Biology, Emory University, Atlanta, Georgia 30322; Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - R Elizabeth Dreggors
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322; Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Emory University, Atlanta, Georgia 30322
| | - Tobias F R Hoffmann
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322; Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Emory University, Atlanta, Georgia 30322.
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17
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Abstract
The kink-turn (k-turn) is a widespread structural motif found in functional RNA species. It typically comprises a three-nucleotide bulge followed by tandem trans sugar edge-Hoogsteen G:A base pairs. It introduces a sharp kink into the axis of duplex RNA, juxtaposing the minor grooves. Cross-strand H-bonds form at the interface, accepted by the conserved adenine nucleobases of the G:A basepairs. Alternative acceptors for one of these divides the k-turns into two conformational classes N3 and N1. The base pair that follows the G:A pairs (3b:3n) determines which conformation is adopted by a given k-turn. k-turns often mediate tertiary contacts in folded RNA species and frequently bind proteins. Common k-turn binding proteins include members of the L7Ae family, such as the human 15·5k protein. A recognition helix within these proteins binds in the widened major groove on the outside of the k-turn, that makes specific H-bonds with the conserved guanine nucleobases of the G:A pairs. L7Ae binds with extremely high affinity, and single-molecule data are consistent with folding by conformational selection. The standard, simple k-turn can be elaborated in a variety of ways, that include the complex k-turns and the k-junctions. In free solution in the absence of added metal ions or protein k-turns do not adopt the tightly-kinked conformation. They undergo folding by the binding of proteins, by the formation of tertiary contacts, and some (but not all) will fold on the addition of metal ions. Whether or not folding occurs in the presence of metal ions depends on local sequence, including the 3b:3n position, and the -1b:-1n position (5' to the bulge). In most cases -1b:-1n = C:G, so that the 3b:3n position is critical since it determines both folding properties and conformation. In general, the selection of these sequence matches a given k-turn to its biological requirements. The k-turn structure is now very well understood, to the point at which they can be used as a building block for the formation of RNA nano-objects, including triangles and squares.
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18
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Lui LM, Uzilov AV, Bernick DL, Corredor A, Lowe TM, Dennis PP. Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. Nucleic Acids Res 2019; 46:5678-5691. [PMID: 29771354 PMCID: PMC6009581 DOI: 10.1093/nar/gky284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.
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Affiliation(s)
- Lauren M Lui
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew V Uzilov
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David L Bernick
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea Corredor
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patrick P Dennis
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
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19
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Paul A, Tiotiu D, Bragantini B, Marty H, Charpentier B, Massenet S, Labialle S. Bcd1p controls RNA loading of the core protein Nop58 during C/D box snoRNP biogenesis. RNA (NEW YORK, N.Y.) 2019; 25:496-506. [PMID: 30700579 PMCID: PMC6426285 DOI: 10.1261/rna.067967.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins (C/D snoRNPs) is guided by conserved trans-acting factors that act collectively to assemble the core proteins SNU13/Snu13, NOP58/Nop58, NOP56/Nop56, FBL/Nop1, and box C/D small nucleolar RNAs (C/D snoRNAs), in human and in yeast, respectively. This finely elaborated process involves the sequential interplay of snoRNP-related proteins and RNA through the formation of transient pre-RNP complexes. BCD1/Bcd1 protein is essential for yeast cell growth and for the specific accumulation of box C/D snoRNAs. In this work, chromatin, RNA, and protein immunoprecipitation assays revealed the ordered loading of several snoRNP-related proteins on immature and mature snoRNA species. Our results identify Bcd1p as an assembly factor of C/D snoRNP biogenesis that is likely recruited cotranscriptionally and that directs the loading of the core protein Nop58 on RNA.
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Affiliation(s)
- Arnaud Paul
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Decebal Tiotiu
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - Hélène Marty
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
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20
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The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution. Biochimie 2019; 164:70-82. [PMID: 30914254 DOI: 10.1016/j.biochi.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/20/2019] [Indexed: 01/09/2023]
Abstract
Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the ability of the RNA to adopt the correct bound conformation. K-turn motifs represent ubiquitous binding platform for proteins found in several cellular environment. This structural motif has an internal three-nucleotide bulge flanked on its 3' side by a G•A/A•G tandem pairs followed by one or two non-Watson-Crick pairs, and on its 5' side by a classical RNA helix. This peculiar arrangement induces a strong curvature of the phosphodiester backbone, which makes it conducive to multiple tertiary interactions. SNU13/Snu13p (Human/Yeast) binds specifically the U14 C/D box snoRNA K-turn sequence motif. This event is the prerequisite to promote the assembly of the RNP, which contains NOP58/Nop58 and NOP56/Nop56 core proteins and the 2'-O-methyl-transferase, Fibrillarin/Nop1p. The U14 small nucleolar RNA is a conserved non-coding RNA found in yeast and vertebrates required for the pre-rRNA maturation and ribose methylation. Here, we report the solution structure of the free U14 snoRNA K-turn motif (kt-U14) as determined by Nuclear Magnetic Resonance. We demonstrate that a major fraction of free kt-U14 adopts a pre-folded conformation similar to protein bound K-turn, even in the absence of divalent ions. In contrast to the kt-U4 or tyrS RNA, kt-U14 displays a sharp bent in the phosphodiester backbone. The U•U and G•A tandem base pairs are formed through weak hydrogen bonds. Finally, we show that the structure of kt-U14 is stabilized upon Snu13p binding. The structure of the free U14 RNA is the first reference example for the canonical motifs of the C/D box snoRNA family.
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21
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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22
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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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23
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Abstract
Advances in genome-wide sequence technologies allow for detailed insights into the complexity of RNA landscapes of organisms from all three domains of life. Recent analyses of archaeal transcriptomes identified interaction and regulation networks of noncoding RNAs in this understudied domain. Here, we review current knowledge of small, noncoding RNAs with important functions for the archaeal lifestyle, which often requires adaptation to extreme environments. One focus is RNA metabolism at elevated temperatures in hyperthermophilic archaea, which reveals elevated amounts of RNA-guided RNA modification and virus defense strategies. Genome rearrangement events result in unique fragmentation patterns of noncoding RNA genes that require elaborate maturation pathways to yield functional transcripts. RNA-binding proteins, e.g., L7Ae and LSm, are important for many posttranscriptional control functions of RNA molecules in archaeal cells. We also discuss recent insights into the regulatory potential of their noncoding RNA partners.
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Affiliation(s)
- José Vicente Gomes-Filho
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
| | - Michael Daume
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
- LOEWE Center for Synthetic Microbiology (Synmikro), 35032 Marburg, Germany
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24
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Nucleolar Division in the Promastigote Stage of Leishmania major Parasite: A Nop56 Point of View. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1641839. [PMID: 30406129 PMCID: PMC6199852 DOI: 10.1155/2018/1641839] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/14/2018] [Accepted: 09/13/2018] [Indexed: 11/23/2022]
Abstract
Nucleogenesis is the cellular event responsible for the formation of the new nucleoli at the end of mitosis. This process depends on the synthesis and processing of ribosomal RNA (rRNA) and, in some eukaryotes, the transfer of nucleolar material contained in prenucleolar bodies (PNBs) to active transcription sites. The lack of a comprehensive description of the nucleolus throughout the cell cycle of the human pathogen Leishmania major prompted us to analyze the distribution of nucleolar protein 56 (Nop56) during interphase and mitosis in the promastigote stage of the parasite. By in silico analysis we show that the orthologue of Nop56 in L. major (LmNop56) contains the three characteristic Nop56 domains and that its predicted three-dimensional structure is also conserved. Fluorescence microscopy observations indicate that the nucleolar localization of LmNop56 is similar, but not identical, to that of the nucleolar protein Elp3b. Notably, unlike other nucleolar proteins, LmNop56 remains associated with the nucleolus in nonproliferative cells. Moreover, epifluorescent images indicate the preservation of the nucleolar structure throughout the closed nuclear division. Experiments performed with the related parasite Trypanosoma brucei show that nucleolar division is carried out by an analogous mechanism.
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Leighton LJ, Bredy TW. Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain. Noncoding RNA 2018; 4:E15. [PMID: 29880782 PMCID: PMC6027130 DOI: 10.3390/ncrna4020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/11/2022] Open
Abstract
Small non-coding RNAs are essential for transcription, translation and gene regulation in all cell types, but are particularly important in neurons, with known roles in neurodevelopment, neuroplasticity and neurological disease. Many small non-coding RNAs are directly involved in the post-transcriptional modification of other RNA species, while others are themselves substrates for modification, or are functionally modulated by modification of their target RNAs. In this review, we explore the known and potential functions of several distinct classes of small non-coding RNAs in the mammalian brain, focusing on the newly recognised interplay between the epitranscriptome and the activity of small RNAs. We discuss the potential for this relationship to influence the spatial and temporal dynamics of gene activation in the brain, and predict that further research in the field of epitranscriptomics will identify interactions between small RNAs and RNA modifications which are essential for higher order brain functions such as learning and memory.
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Affiliation(s)
- Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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Filippova JA, Semenov DV, Juravlev ES, Komissarov AB, Richter VA, Stepanov GA. Modern Approaches for Identification of Modified Nucleotides in RNA. BIOCHEMISTRY (MOSCOW) 2018; 82:1217-1233. [PMID: 29223150 DOI: 10.1134/s0006297917110013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.
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Affiliation(s)
- J A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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Gopalan V, Jarrous N, Krasilnikov AS. Chance and necessity in the evolution of RNase P. RNA (NEW YORK, N.Y.) 2018; 24:1-5. [PMID: 28971852 PMCID: PMC5733564 DOI: 10.1261/rna.063107.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/22/2017] [Indexed: 05/20/2023]
Abstract
RNase P catalyzes 5'-maturation of tRNAs in all three domains of life. This primary function is accomplished by either a ribozyme-centered ribonucleoprotein (RNP) or a protein-only variant (with one to three polypeptides). The large, multicomponent archaeal and eukaryotic RNase P RNPs appear disproportionate to the simplicity of their role in tRNA 5'-maturation, prompting the question of why the seemingly gratuitously complex RNP forms of RNase P were not replaced with simpler protein counterparts. Here, motivated by growing evidence, we consider the hypothesis that the large RNase P RNP was retained as a direct consequence of multiple roles played by its components in processes that are not related to the canonical RNase P function.
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Affiliation(s)
- Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Nayef Jarrous
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Andrey S Krasilnikov
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Ashraf S, Huang L, Lilley DMJ. Sequence determinants of the folding properties of box C/D kink-turns in RNA. RNA (NEW YORK, N.Y.) 2017; 23:1927-1935. [PMID: 28956757 PMCID: PMC5689011 DOI: 10.1261/rna.063453.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 05/20/2023]
Abstract
Folding properties differ markedly between kink-turns (k-turns) that have different biological functions. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. In contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.
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Affiliation(s)
- Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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Gauernack AS, Lassek C, Hou L, Dzieciolowski J, Evguenieva-Hackenberg E, Klug G. Nop5 interacts with the archaeal RNA exosome. FEBS Lett 2017; 591:4039-4048. [PMID: 29159940 DOI: 10.1002/1873-3468.12915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 01/02/2023]
Abstract
The archaeal exosome, a protein complex responsible for phosphorolytic degradation and tailing of RNA, has an RNA-binding platform containing Rrp4, Csl4, and DnaG. Aiming to detect novel interaction partners of the exosome, we copurified Nop5, which is a part of an rRNA methylating ribonucleoprotein complex, with the exosome of Sulfolobus solfataricus grown to a late stationary phase. We demonstrated the capability of Nop5 to bind to the exosome with a homotrimeric Rrp4-cap and to increase the proportion of polyadenylated RNAin vitro, suggesting that Nop5 is a dual-function protein. Since tailing of RNA probably serves to enhance RNA degradation, association of Nop5 with the archaeal exosome in the stationary phase may enhance tailing and degradation of RNA as survival strategy.
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Affiliation(s)
- A Susann Gauernack
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Germany
| | - Christian Lassek
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Germany
| | - Linlin Hou
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Germany
| | - Julia Dzieciolowski
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Germany
| | | | - Gabriele Klug
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Germany
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30
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Huang L, Ashraf S, Wang J, Lilley DM. Control of box C/D snoRNP assembly by N 6-methylation of adenine. EMBO Rep 2017; 18:1631-1645. [PMID: 28623187 PMCID: PMC5579392 DOI: 10.15252/embr.201743967] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/03/2023] Open
Abstract
N6-methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N6-methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N6-methylation of adenine prevents the formation of trans Hoogsteen-sugar A·G base pairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A·G base pairs (but not Watson-Crick base pairs) are more susceptible to disruption by N6mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared base pair with guanine and mediates a key tertiary interaction.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - David Mj Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
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31
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Tomkuvienė M, Ličytė J, Olendraitė I, Liutkevičiūtė Z, Clouet-d'Orval B, Klimašauskas S. Archaeal fibrillarin-Nop5 heterodimer 2'- O-methylates RNA independently of the C/D guide RNP particle. RNA (NEW YORK, N.Y.) 2017; 23:1329-1337. [PMID: 28576826 PMCID: PMC5558902 DOI: 10.1261/rna.059832.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/19/2017] [Indexed: 06/01/2023]
Abstract
Archaeal fibrillarin (aFib) is a well-characterized S-adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a Pyrococcus abyssi aFib-Nop5 heterodimer can alone perform SAM-dependent 2'-O-methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2'-O-methylated positions in the 16S rRNA of P. abyssi, positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib-Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution.
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MESH Headings
- Archaea/genetics
- Archaea/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Methylation
- Nucleic Acid Conformation
- Protein Binding
- Protein Multimerization
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/metabolism
- Substrate Specificity
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Affiliation(s)
- Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Ingrida Olendraitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Zita Liutkevičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et Génétique Moléculaires UMR 5100, CNRS, Université de Toulouse, F-31062 Toulouse, France
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
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32
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Abstract
L7Ae is a universal archaeal protein that recognizes and stabilizes kink-turn (k-turn) motifs in RNA substrates. These structural motifs are widespread in nature and are found in many functional RNA species, including ribosomal RNAs. Synthetic biology approaches utilize L7Ae/k-turn interactions to control gene expression in eukaryotes. Here, we present results of comprehensive RNA immunoprecipitation sequencing (RIP-Seq) analysis of genomically tagged L7Ae from the hyperthermophilic archaeon Sulfolobus acidocaldarius. A large set of interacting noncoding RNAs was identified. In addition, several mRNAs, including the l7ae transcript, were found to contain k-turn motifs that facilitate L7Ae binding. In vivo studies showed that L7Ae autoregulates the translation of its mRNA by binding to a k-turn motif present in the 5′ untranslated region (UTR). A green fluorescent protein (GFP) reporter system was established in Escherichia coli and verified conservation of L7Ae-mediated feedback regulation in Archaea. Mobility shift assays confirmed binding to a k-turn in the transcript of nop5-fibrillarin, suggesting that the expression of all C/D box sRNP core proteins is regulated by L7Ae. These studies revealed that L7Ae-mediated gene regulation evolved in archaeal organisms, generating new tools for the modulation of synthetic gene circuits in bacteria. L7Ae is an essential archaeal protein that is known to structure ribosomal RNAs and small RNAs (sRNAs) by binding to their kink-turn motifs. Here, we utilized RIP-Seq methodology to achieve a first global analysis of RNA substrates for L7Ae. Several novel interactions with noncoding RNA molecules (e.g., with the universal signal recognition particle RNA) were discovered. In addition, L7Ae was found to bind to mRNAs, including its own transcript’s 5′ untranslated region. This feedback-loop control is conserved in most archaea and was incorporated into a reporter system that was utilized to control gene expression in bacteria. These results demonstrate that L7Ae-mediated gene regulation evolved originally in archaeal organisms. The feedback-controlled reporter gene system can easily be adapted for synthetic biology approaches that require strict gene expression control.
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Massenet S, Bertrand E, Verheggen C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol 2017; 14:680-692. [PMID: 27715451 PMCID: PMC5519232 DOI: 10.1080/15476286.2016.1243646] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022] Open
Abstract
Box C/D and box H/ACA snoRNAs are abundant non-coding RNAs that localize in the nucleolus and mostly function as guides for nucleotide modifications. While a large pool of snoRNAs modifies rRNAs, an increasing number of snoRNAs could also potentially target mRNAs. ScaRNAs belong to a family of specific RNAs that localize in Cajal bodies and that are structurally similar to snoRNAs. Most scaRNAs are involved in snRNA modification, while telomerase RNA, which contains H/ACA motifs, functions in telomeric DNA synthesis. In this review, we describe how box C/D and H/ACA snoRNAs are processed and assembled with core proteins to form functional RNP particles. Their biogenesis involve several transport factors that first direct pre-snoRNPs to Cajal bodies, where some processing steps are believed to take place, and then to nucleoli. Assembly of core proteins involves the HSP90/R2TP chaperone-cochaperone system for both box C/D and H/ACA RNAs, but also several factors specific for each family. These assembly factors chaperone unassembled core proteins, regulate the formation and disassembly of pre-snoRNP intermediates, and control the activity of immature particles. The AAA+ ATPase RUVBL1 and RUVBL2 belong to the R2TP co-chaperones and play essential roles in snoRNP biogenesis, as well as in the formation of other macro-molecular complexes. Despite intensive research, their mechanisms of action are still incompletely understood.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS, 9 Avenue de la forêt de Haye, 54505 Vandoeuvre-les-Nancy Cedex, France, Université de Lorraine, Campus Biologie –Santé, CS 50184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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Henras AK, Plisson-Chastang C, Humbert O, Romeo Y, Henry Y. Synthesis, Function, and Heterogeneity of snoRNA-Guided Posttranscriptional Nucleoside Modifications in Eukaryotic Ribosomal RNAs. Enzymes 2017; 41:169-213. [PMID: 28601222 DOI: 10.1016/bs.enz.2017.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosomal RNAs contain numerous 2'-O-methylated nucleosides and pseudouridines. Methylation of the 2' oxygen of ribose moieties and isomerization of uridines into pseudouridines are catalyzed by C/D and H/ACA small nucleolar ribonucleoprotein particles, respectively. We review the composition, structure, and mode of action of archaeal and eukaryotic C/D and H/ACA particles. Most rRNA modifications cluster in functionally crucial regions of the rRNAs, suggesting they play important roles in translation. Some of these modifications promote global translation efficiency or modulate translation fidelity. Strikingly, recent quantitative nucleoside modification profiling methods have revealed that a subset of modification sites is not always fully modified. The finding of such ribosome heterogeneity is in line with the concept of specialized ribosomes that could preferentially translate specific mRNAs. This emerging concept is supported by findings that some human diseases are caused by defects in the rRNA modification machinery correlated with a significant alteration of IRES-dependent translation.
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
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35
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Seistrup KH, Rose S, Birkedal U, Nielsen H, Huber H, Douthwaite S. Bypassing rRNA methylation by RsmA/Dim1during ribosome maturation in the hyperthermophilic archaeon Nanoarchaeum equitans. Nucleic Acids Res 2017; 45:2007-2015. [PMID: 28204608 PMCID: PMC5389701 DOI: 10.1093/nar/gkw839] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/10/2016] [Indexed: 12/16/2022] Open
Abstract
In all free-living organisms a late-stage checkpoint in the biogenesis of the small ribosomal subunit involves rRNA modification by an RsmA/Dim1 methyltransferase. The hyperthermophilic archaeon Nanoarchaeum equitans, whose existence is confined to the surface of a second archaeon, Ignicoccus hospitalis, lacks an RsmA/Dim1 homolog. We demonstrate here that the I. hospitalis host possesses the homolog Igni_1059, which dimethylates the N6-positions of two invariant adenosines within helix 45 of 16S rRNA in a manner identical to other RsmA/Dim1 enzymes. However, Igni_1059 is not transferred from I. hospitalis to N. equitans across their fused cell membrane structures and the corresponding nucleotides in N. equitans 16S rRNA remain unmethylated. An alternative mechanism for ribosomal subunit maturation in N. equitans is suggested by sRNA interactions that span the redundant RsmA/Dim1 site to introduce 2΄-O-ribose methylations within helices 44 and 45 of the rRNA.
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Affiliation(s)
- Kenneth H. Seistrup
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Simon Rose
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ulf Birkedal
- Department of Cellular & Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Henrik Nielsen
- Department of Cellular & Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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36
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Abstract
Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.
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Affiliation(s)
- Zuxiao Yang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinzhong Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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37
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Shubina MY, Musinova YR, Sheval EV. Nucleolar methyltransferase fibrillarin: Evolution of structure and functions. BIOCHEMISTRY (MOSCOW) 2016; 81:941-50. [DOI: 10.1134/s0006297916090030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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38
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Quinternet M, Chagot ME, Rothé B, Tiotiu D, Charpentier B, Manival X. Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species. Structure 2016; 24:1693-1706. [PMID: 27594683 DOI: 10.1016/j.str.2016.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/15/2022]
Abstract
Box C/D small nucleolar ribonucleoparticles (snoRNPs) support 2'-O-methylation of several target RNAs. They share a common set of four core proteins (SNU13, NOP58, NOP56, and FBL) that are assembled on different guide small nucleolar RNAs. Assembly of these entities involves additional protein factors that are absent in the mature active particle. In this context, the platform protein NUFIP1/Rsa1 establishes direct and simultaneous contacts with core proteins and with the components of the assembly machinery. Here, we solve the nuclear magnetic resonance (NMR) structure of a complex resulting from interaction between protein fragments of human NUFIP1 and its cofactor ZNHIT3, and emphasize their imbrication. Using yeast two-hybrid and complementation assays, protein co-expression, isothermal titration calorimetry, and NMR, we demonstrate that yeast and human complexes involving NUFIP1/Rsa1p, ZNHIT3/Hit1p, and SNU13/Snu13p share strong structural similarities, suggesting that the initial steps of the box C/D snoRNP assembly process are conserved among species.
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Affiliation(s)
- Marc Quinternet
- FR CNRS-3209 Bioingénierie Moléculaire, Cellulaire et Thérapeutique (BMCT), CNRS, Université de Lorraine, Biopôle, Campus Biologie-Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France; Ecole polytechnique fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Decebal Tiotiu
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France.
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Yip WSV, Shigematsu H, Taylor DW, Baserga SJ. Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs. Nucleic Acids Res 2016; 44:8976-8989. [PMID: 27342279 PMCID: PMC5062973 DOI: 10.1093/nar/gkw576] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 06/15/2016] [Indexed: 01/01/2023] Open
Abstract
Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2′-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture.
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Affiliation(s)
- W S Vincent Yip
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Hideki Shigematsu
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA RIKEN Center for Life Science Technology, Yokohama, Kanagawa 230-0045, Japan
| | - David W Taylor
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Department of Genetics, Yale University, New Haven, CT 06520, USA Department of Therapeutic Radiology, Yale University, New Haven, CT 06520, USA
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Graziadei A, Masiewicz P, Lapinaite A, Carlomagno T. Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency. RNA (NEW YORK, N.Y.) 2016; 22:764-772. [PMID: 26925607 PMCID: PMC4836650 DOI: 10.1261/rna.054320.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/21/2016] [Indexed: 06/01/2023]
Abstract
RNA modifications confer complexity to the 4-nucleotide polymer; nevertheless, their exact function is mostly unknown. rRNA 2'-O-ribose methylation concentrates to ribosome functional sites and is important for ribosome biogenesis. The methyl group is transferred to rRNA by the box C/D RNPs: The rRNA sequence to be methylated is recognized by a complementary sequence on the guide RNA, which is part of the enzyme. In contrast to their eukaryotic homologs, archaeal box C/D enzymes can be assembled in vitro and are used to study the mechanism of 2'-O-ribose methylation. In Archaea, each guide RNA directs methylation to two distinct rRNA sequences, posing the question whether this dual architecture of the enzyme has a regulatory role. Here we use methylation assays and low-resolution structural analysis with small-angle X-ray scattering to study the methylation reaction guided by the sR26 guide RNA fromPyrococcus furiosus We find that the methylation efficacy at sites D and D' differ substantially, with substrate D' turning over more efficiently than substrate D. This observation correlates well with structural data: The scattering profile of the box C/D RNP half-loaded with substrate D' is similar to that of the holo complex, which has the highest activity. Unexpectedly, the guide RNA secondary structure is not responsible for the functional difference at the D and D' sites. Instead, this difference is recapitulated by the nature of the first base pair of the guide-substrate duplex. We suggest that substrate turnover may occur through a zip mechanism that initiates at the 5'-end of the product.
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Affiliation(s)
- Andrea Graziadei
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany
| | - Pawel Masiewicz
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany
| | - Audrone Lapinaite
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany
| | - Teresa Carlomagno
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany Leibniz University Hannover, Centre for Biomolecular Drug Research, D-30167 Hannover, Germany Helmholtz Centre for Infection Research, Group of Structural Chemistry, D-38124 Braunschweig, Germany
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Dennis PP, Tripp V, Lui L, Lowe T, Randau L. C/D box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules. BMC Genomics 2015; 16:632. [PMID: 26296872 PMCID: PMC4644070 DOI: 10.1186/s12864-015-1839-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/13/2015] [Indexed: 11/26/2022] Open
Abstract
Background In archaea and eukaryotes, ribonucleoprotein complexes containing small C/D box s(no)RNAs use base pair complementarity to target specific sites within ribosomal RNA for 2'-O-ribose methylation. These modifications aid in the folding and stabilization of nascent rRNA molecules and their assembly into ribosomal particles. The genomes of hyperthermophilic archaea encode large numbers of C/D box sRNA genes, suggesting an increased necessity for rRNA stabilization at extreme growth temperatures. Results We have identified the complete sets of C/D box sRNAs from seven archaea using RNA-Seq methodology. In total, 489 C/D box sRNAs were identified, each containing two guide regions. A combination of computational and manual analyses predicts 719 guide interactions with 16S and 23S rRNA molecules. This first pan-archaeal description of guide sequences identifies (i) modified rRNA nucleotides that are frequently conserved between species and (ii) regions within rRNA that are hotspots for 2'-O-methylation. Gene duplication, rearrangement, mutational drift and convergent evolution of sRNA genes and guide sequences were observed. In addition, several C/D box sRNAs were identified that use their two guides to target locations distant in the rRNA sequence but close in the secondary and tertiary structure. We propose that they act as RNA chaperones and facilitate complex folding events between distant sequences. Conclusions This pan-archaeal analysis of C/D box sRNA guide regions identified conserved patterns of rRNA 2'-O-methylation in archaea. The interaction between the sRNP complexes and the nascent rRNA facilitates proper folding and the methyl modifications stabilize higher order rRNA structure within the assembled ribosome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1839-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick P Dennis
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany. .,Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA.
| | - Vanessa Tripp
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany.
| | - Lauren Lui
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Todd Lowe
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany.
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Rodriguez-Corona U, Sobol M, Rodriguez-Zapata LC, Hozak P, Castano E. Fibrillarin from Archaea to human. Biol Cell 2015; 107:159-74. [PMID: 25772805 DOI: 10.1111/boc.201400077] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022]
Abstract
Fibrillarin is an essential protein that is well known as a molecular marker of transcriptionally active RNA polymerase I. Fibrillarin methyltransferase activity is the primary known source of methylation for more than 100 methylated sites involved in the first steps of preribosomal processing and required for structural ribosome stability. High expression levels of fibrillarin have been observed in several types of cancer cells, particularly when p53 levels are reduced, because p53 is a direct negative regulator of fibrillarin transcription. Here, we show fibrillarin domain conservation, structure and interacting molecules in different cellular processes as well as with several viral proteins during virus infection.
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Affiliation(s)
- Ulises Rodriguez-Corona
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Luis Carlos Rodriguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Enrique Castano
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
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Lai SM, Lai LB, Foster MP, Gopalan V. The L7Ae protein binds to two kink-turns in the Pyrococcus furiosus RNase P RNA. Nucleic Acids Res 2014; 42:13328-38. [PMID: 25361963 PMCID: PMC4245976 DOI: 10.1093/nar/gku994] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The RNA-binding protein L7Ae, known for its role in translation (as part of ribosomes) and RNA modification (as part of sn/oRNPs), has also been identified as a subunit of archaeal RNase P, a ribonucleoprotein complex that employs an RNA catalyst for the Mg2+-dependent 5′ maturation of tRNAs. To better understand the assembly and catalysis of archaeal RNase P, we used a site-specific hydroxyl radical-mediated footprinting strategy to pinpoint the binding sites of Pyrococcus furiosus (Pfu) L7Ae on its cognate RNase P RNA (RPR). L7Ae derivatives with single-Cys substitutions at residues in the predicted RNA-binding interface (K42C/C71V, R46C/C71V, V95C/C71V) were modified with an iron complex of EDTA-2-aminoethyl 2-pyridyl disulfide. Upon addition of hydrogen peroxide and ascorbate, these L7Ae-tethered nucleases were expected to cleave the RPR at nucleotides proximal to the EDTA-Fe–modified residues. Indeed, footprinting experiments with an enzyme assembled with the Pfu RPR and five protein cofactors (POP5, RPP21, RPP29, RPP30 and L7Ae–EDTA-Fe) revealed specific RNA cleavages, localizing the binding sites of L7Ae to the RPR's catalytic and specificity domains. These results support the presence of two kink-turns, the structural motifs recognized by L7Ae, in distinct functional domains of the RPR and suggest testable mechanisms by which L7Ae contributes to RNase P catalysis.
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Affiliation(s)
- Stella M Lai
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Lien B Lai
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Rothé B, Saliou JM, Quinternet M, Back R, Tiotiu D, Jacquemin C, Loegler C, Schlotter F, Peña V, Eckert K, Moréra S, Dorsselaer AV, Branlant C, Massenet S, Sanglier-Cianférani S, Manival X, Charpentier B. Protein Hit1, a novel box C/D snoRNP assembly factor, controls cellular concentration of the scaffolding protein Rsa1 by direct interaction. Nucleic Acids Res 2014; 42:10731-47. [PMID: 25170085 PMCID: PMC4176330 DOI: 10.1093/nar/gku612] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 01/09/2023] Open
Abstract
Biogenesis of eukaryotic box C/D small nucleolar ribonucleoprotein particles (C/D snoRNPs) involves conserved trans-acting factors, which are proposed to facilitate the assembly of the core proteins Snu13p/15.5K, Nop58p/NOP58, Nop56p/NOP56 and Nop1p/Fibrillarin on box C/D small nucleolar RNAs (C/D snoRNAs). In yeast, protein Rsa1 acts as a platform, interacting with both the RNA-binding core protein Snu13 and protein Pih1 of the Hsp82-R2TP chaperone complex. In this work, a proteomic approach coupled with functional and structural studies identifies protein Hit1 as a novel Rsa1p-interacting partner involved in C/D snoRNP assembly. Hit1p contributes to in vivo C/D snoRNA stability and pre-RNA maturation kinetics. It associates with U3 snoRNA precursors and influences its 3'-end processing. Remarkably, Hit1p is required to maintain steady-state levels of Rsa1p. This stabilizing activity is likely to be general across eukaryotic species, as the human protein ZNHIT3(TRIP3) showing sequence homology with Hit1p regulates the abundance of NUFIP1, the Rsa1p functional homolog. The nuclear magnetic resonance solution structure of the Rsa1p317-352-Hit1p70-164 complex reveals a novel mode of protein-protein association explaining the strong stability of the Rsa1p-Hit1p complex. Our biochemical data show that C/D snoRNAs and the core protein Nop58 can interact with the purified Snu13p-Rsa1p-Hit1p heterotrimer.
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Affiliation(s)
- Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Jean-Michel Saliou
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Marc Quinternet
- FR CNRS-3209 Bioingénierie Moléculaire, Cellulaire et Thérapeutique (BMCT), CNRS, Université de Lorraine, Biopôle, Campus Biologie Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Régis Back
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Decebal Tiotiu
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Clémence Jacquemin
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Christine Loegler
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Vlad Peña
- Max-Planck-Institut für biophysikalische Chemie, Abtl. Röntgenkristallographie, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kelvin Eckert
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, 1 Avenue de Terrasse, 91198 Gif-sur Yvette, France
| | - Solange Moréra
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, 1 Avenue de Terrasse, 91198 Gif-sur Yvette, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
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Kakihara Y, Makhnevych T, Zhao L, Tang W, Houry WA. Nutritional status modulates box C/D snoRNP biogenesis by regulated subcellular relocalization of the R2TP complex. Genome Biol 2014; 15:404. [PMID: 25060708 PMCID: PMC4165372 DOI: 10.1186/s13059-014-0404-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Box C/D snoRNPs, which are typically composed of box C/D snoRNA and the four core protein components Nop1, Nop56, Nop58, and Snu13, play an essential role in the modification and processing of pre-ribosomal RNA. The highly conserved R2TP complex, comprising the proteins Rvb1, Rvb2, Tah1, and Pih1, has been shown to be required for box C/D snoRNP biogenesis and assembly; however, the molecular basis of R2TP chaperone-like activity is not yet known. RESULTS Here, we describe an unexpected finding in which the activity of the R2TP complex is required for Nop58 protein stability and is controlled by the dynamic subcellular redistribution of the complex in response to growth conditions and nutrient availability. In growing cells, the complex localizes to the nucleus and interacts with box C/D snoRNPs. This interaction is significantly reduced in poorly growing cells as R2TP predominantly relocalizes to the cytoplasm. The R2TP-snoRNP interaction is mainly mediated by Pih1. CONCLUSIONS The R2TP complex exerts a novel regulation on box C/D snoRNP biogenesis that affects their assembly and consequently pre-rRNA maturation in response to different growth conditions.
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Ye W, Yang J, Yu Q, Wang W, Hancy J, Luo R, Chen HF. Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations. Phys Chem Chem Phys 2014; 15:18510-22. [PMID: 24072031 DOI: 10.1039/c3cp53145g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The kink-turn sRNA motif in archaea, whose combination with protein L7Ae initializes the assembly of small ribonucleoprotein particles (sRNPs), plays a key role in ribosome maturation and the translation process. Although many studies have been reported on this motif, the mechanism of sRNA folding coupled with protein binding is still poorly understood. Here, room and high temperature molecular dynamics (MD) simulations were performed on the complex of 25-nt kink-turn sRNA and L7Ae. The average RMSD values between the bound and corresponding apo structures and Kolmogorov-Smirnov P test analysis indicate that sRNA may follow an induced fit mechanism upon binding with L7Ae, both locally and globally. These conclusions are further supported by high-temperature unfolding kinetic analysis. Principal component analysis (PCA) found both closing and opening motions of the kink-turn sRNA. This might play a key role in the sRNP assembly and methylation catalysis. These combined computational methods can be used to study the specific recognition of other sRNAs and proteins.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
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Abstract
snoRNAs (small nucleolar RNAs) constitute one of the largest and best-studied classes of non-coding RNAs that confer enzymatic specificity. With associated proteins, these snoRNAs form ribonucleoprotein complexes that can direct 2'-O-methylation or pseudouridylation of target non-coding RNAs. Aided by computational methods and high-throughput sequencing, new studies have expanded the diversity of known snoRNA functions. Complexes incorporating snoRNAs have dynamic specificity, and include diverse roles in RNA silencing, telomerase maintenance and regulation of alternative splicing. Evidence that dysregulation of snoRNAs can cause human disease, including cancer, indicates that the full scope of snoRNA roles remains an unfinished story. The diversity in structure, genomic origin and function between snoRNAs found in different complexes and among different phyla illustrates the surprising plasticity of snoRNAs in evolution. The ability of snoRNAs to direct highly specific interactions with other RNAs is a consistent thread in their newly discovered functions. Because they are ubiquitous throughout Eukarya and Archaea, it is likely they were a feature of the last common ancestor of these two domains, placing their origin over two billion years ago. In the present chapter, we focus on recent advances in our understanding of these ancient, but functionally dynamic RNA-processing machines.
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Ozoe A, Sone M, Fukushima T, Kataoka N, Chida K, Asano T, Hakuno F, Takahashi SI. Insulin receptor substrate-1 associates with small nucleolar RNA which contributes to ribosome biogenesis. Front Endocrinol (Lausanne) 2014; 5:24. [PMID: 24624118 PMCID: PMC3941584 DOI: 10.3389/fendo.2014.00024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 02/14/2014] [Indexed: 11/29/2022] Open
Abstract
Insulin receptor substrates (IRSs) are well known to play crucial roles in mediating intracellular signals of insulin-like growth factors (IGFs)/insulin. Previously, we showed that IRS-1 forms high molecular mass complexes containing RNAs. To identify RNAs in IRS-1 complexes, we performed ultraviolet (UV) cross-linking and immunoprecipitation analysis using HEK293 cells expressing FLAG-IRS-1 and FLAG-IRS-2. We detected the radioactive signals in the immunoprecipitates of FLAG-IRS-1 proportional to the UV irradiation, but not in the immunoprecipitates of FLAG-IRS-2, suggesting the direct contact of RNAs with IRS-1. RNAs cross-linked to IRS-1 were then amplified by RT-PCR, followed by sequence analysis. We isolated sequence tags attributed to 25 messenger RNAs and 8 non-coding RNAs, including small nucleolar RNAs (snoRNAs). We focused on the interaction of IRS-1 with U96A snoRNA (U96A) and its host Rack1 (receptor for activated C kinase 1) pre-mRNA. We confirmed the interaction of IRS-1 with U96A, and with RACK1 pre-mRNA by immunoprecipitation with IRS-1 followed by Northern blotting or RT-PCR analyses. Mature U96A in IRS-1(-/-) mouse embryonic fibroblasts was quantitatively less than WT. We also found that a part of nuclear IRS-1 is localized in the Cajal body, a nuclear subcompartment where snoRNA mature. The unanticipated function of IRS-1 in snoRNA biogenesis highlights the potential of RNA-associated IRS-1 complex to open a new line of investigation to dissect the novel mechanisms regulating IGFs/insulin-mediated biological events.
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Affiliation(s)
- Atsufumi Ozoe
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Meri Sone
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Fukushima
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naoyuki Kataoka
- Laboratory for Malignancy Control Research, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuhiro Chida
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoichiro Asano
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Fumihiko Hakuno
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin-Ichiro Takahashi
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- *Correspondence: Shin-Ichiro Takahashi, Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan e-mail:
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Rothé B, Back R, Quinternet M, Bizarro J, Robert MC, Blaud M, Romier C, Manival X, Charpentier B, Bertrand E, Branlant C. Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly. Nucleic Acids Res 2013; 42:2015-36. [PMID: 24234454 PMCID: PMC3919607 DOI: 10.1093/nar/gkt1091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The yeast Snu13p protein and its 15.5K human homolog both bind U4 snRNA and box C/D snoRNAs. They also bind the Rsa1p/NUFIP assembly factor, proposed to scaffold immature snoRNPs and to recruit the Hsp90-R2TP chaperone complex. However, the nature of the Snu13p/15.5K–Rsa1p/NUFIP interaction and its exact role in snoRNP assembly remained to be elucidated. By using biophysical, molecular and imaging approaches, here, we identify residues needed for Snu13p/15.5K–Rsa1p/NUFIP interaction. By NMR structure determination and docking approaches, we built a 3D model of the Snup13p–Rsa1p interface, suggesting that residues R249, R246 and K250 in Rsa1p and E72 and D73 in Snu13p form a network of electrostatic interactions shielded from the solvent by hydrophobic residues from both proteins and that residue W253 of Rsa1p is inserted in a hydrophobic cavity of Snu13p. Individual mutations of residues in yeast demonstrate the functional importance of the predicted interactions for both cell growth and snoRNP formation. Using archaeal box C/D sRNP 3D structures as templates, the association of Snu13p with Rsa1p is predicted to be exclusive of interactions in active snoRNPs. Rsa1p and NUFIP may thus prevent premature activity of pre-snoRNPs, and their removal may be a key step for active snoRNP production.
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Affiliation(s)
- Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 184, 54505 Vandœuvre-lès-Nancy, France, FR CNRS-3209 (Ingénierie Moléculaire et Thérapeutique), CNRS, Université de Lorraine, Faculté de Médecine, Bâtiment Biopôle, BP 184, 54505 Vandœuvre-lès-Nancy Cedex, France, Equipe labellisée Ligue contre le Cancer, IGMM (Institut de Génétique Moléculaire de Montpellier), Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5535, Montpellier Cedex 5, France and IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, Université de Strasbourg, CNRS, INSERM, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
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