101
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Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 2007; 8:209-20. [PMID: 17318225 DOI: 10.1038/nrm2124] [Citation(s) in RCA: 552] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advances have fuelled rapid growth in our appreciation of the tremendous number, diversity and biological importance of non-coding (nc)RNAs. Because ncRNAs typically function as ribonucleoprotein (RNP) complexes and not as naked RNAs, understanding their biogenesis is crucial to comprehending their regulation and function. The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs.
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MESH Headings
- Animals
- Cell Nucleus/metabolism
- Humans
- Nucleic Acid Conformation
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nucleolar/metabolism
- Transcription, Genetic
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Affiliation(s)
- A Gregory Matera
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106-4955, USA.
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102
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Cléry A, Bourguignon-Igel V, Allmang C, Krol A, Branlant C. An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery. Nucleic Acids Res 2007; 35:1868-84. [PMID: 17332014 PMCID: PMC1874613 DOI: 10.1093/nar/gkm066] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
By binding to SECIS elements located in the 3′-UTR of selenoprotein mRNAs, the protein SBP2 plays a key role in the assembly of the selenocysteine incorporation machinery. SBP2 contains an L7Ae/L30 RNA-binding domain similar to that of protein 15.5K/Snu13p, which binds K-turn motifs with a 3-nt bulge loop closed by a tandem of G.A and A.G pairs. Here, by SELEX experiments, we demonstrate the capacity of SBP2 to bind such K-turn motifs with a protruding U residue. However, we show that conversion of the bulge loop into an internal loop reinforces SBP2 affinity and to a greater extent RNP stability. Opposite variations were found for Snu13p. Accordingly, footprinting assays revealed strong contacts of SBP2 with helices I and II and the 5′-strand of the internal loop, as opposed to the loose interaction of Snu13p. Our data also identifies new determinants for SBP2 binding which are located in helix II. Among the L7Ae/L30 family members, these determinants are unique to SBP2. Finally, in accordance with functional data on SECIS elements, the identity of residues at positions 2 and 3 in the loop influences SBP2 affinity. Altogether, the data provide a very precise definition of the SBP2 RNA specificity.
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Affiliation(s)
- A. Cléry
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire – UMR 7567 CNRS-UHP, Nancy Université, Faculté des Sciences et Techniques – BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France and Architecture et Réactivité de l'arN – CNRS-Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire 15 Rue René Descartes, 67084 Strasbourg Cedex, France
| | - V. Bourguignon-Igel
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire – UMR 7567 CNRS-UHP, Nancy Université, Faculté des Sciences et Techniques – BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France and Architecture et Réactivité de l'arN – CNRS-Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire 15 Rue René Descartes, 67084 Strasbourg Cedex, France
| | - C. Allmang
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire – UMR 7567 CNRS-UHP, Nancy Université, Faculté des Sciences et Techniques – BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France and Architecture et Réactivité de l'arN – CNRS-Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire 15 Rue René Descartes, 67084 Strasbourg Cedex, France
| | - A. Krol
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire – UMR 7567 CNRS-UHP, Nancy Université, Faculté des Sciences et Techniques – BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France and Architecture et Réactivité de l'arN – CNRS-Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire 15 Rue René Descartes, 67084 Strasbourg Cedex, France
| | - C. Branlant
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire – UMR 7567 CNRS-UHP, Nancy Université, Faculté des Sciences et Techniques – BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France and Architecture et Réactivité de l'arN – CNRS-Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire 15 Rue René Descartes, 67084 Strasbourg Cedex, France
- *To whom the correspondence should be addressed. 33 38368430333 383684307
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103
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Reichow SL, Hamma T, Ferré-D'Amaré AR, Varani G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res 2007; 35:1452-64. [PMID: 17284456 PMCID: PMC1865073 DOI: 10.1093/nar/gkl1172] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequence-specific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose-2′-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the core archaeal sRNP proteins have been determined and their assembly pathways delineated. Furthermore, the recent structure of an H/ACA complex has revealed the organization of a complete sRNP. Combined with current biochemical data, these structures offer insight into the highly homologous eukaryotic snoRNPs.
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Affiliation(s)
- Steve L. Reichow
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Tomoko Hamma
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Adrian R. Ferré-D'Amaré
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
- *To whom correspondence should be addressed. +(206) 543 1610+(206) 685 8665
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104
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Decatur WA, Liang XH, Piekna-Przybylska D, Fournier MJ. Identifying effects of snoRNA-guided modifications on the synthesis and function of the yeast ribosome. Methods Enzymol 2007; 425:283-316. [PMID: 17673089 DOI: 10.1016/s0076-6879(07)25013-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The small nucleolar RNAs (snoRNAs) are associated with proteins in ribonucleoprotein complexes called snoRNPs ("snorps"). These complexes create modified nucleotides in preribosomal RNA and other RNAs and participate in nucleolytic cleavages of pre-rRNA. The various reactions occur in site-specific fashion, and the mature rRNAs are ultimately incorporated into cytoplasmic ribosomes. Most snoRNAs exist in two structural classes, and most members in each class are involved in nucleotide modification reactions. Guide snoRNAs in the "box C/D" class target methylation of the 2'-hydroxyl moiety, to form 2'-O-methylated nucleotides (Nm), whereas guide snoRNAs in the "box H/ACA" class target specific uridines for conversion to pseudouridine (Psi). The rRNA nucleotides modified in this manner are numerous, totaling approximately 100 in yeast and twice that number in humans. Although the chemistry of the modifications and the factors involved in their formation are largely explained, very little is known about the influence of the copious snoRNA-guided nucleotide modifications on rRNA activity and ribosome function. Among eukaryotic organisms the sites of rRNA modification and the corresponding guide snoRNAs have been best characterized in S. cerevisiae, making this a model organism for analyzing the consequences of modification. This chapter presents approaches to characterizing rRNA modification effects in yeast and includes strategies for evaluating a variety of specific rRNA functions. To aid in planning, a package of bioinformatics tools is described that enables investigators to correlate guide function with targeted ribosomal sites in several contexts. Genetic procedures are presented for depleting modifications at one or more rRNA sites, including ablation of all Nm or Psi modifications made by snoRNPs, and for introducing modifications at novel sites. Methods are also included for characterizing modification effects on cell growth, antibiotic sensitivity, rRNA processing, formation of various rRNP complexes, translation activity, and rRNA structure within the ribosome.
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Affiliation(s)
- Wayne A Decatur
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
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105
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Piekna-Przybylska D, Liu B, Fournier MJ. The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes. Methods Enzymol 2007; 425:317-53. [PMID: 17673090 DOI: 10.1016/s0076-6879(07)25014-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When isolating ribonucleoprotein (RNP) complexes by an affinity selection approach, tagging the RNA component can prove to be strategically important. This is especially true for purifying single types of snoRNPs, because in most cases the snoRNA is thought to be the only unique component. Here, we present a general strategy for selecting specific snoRNPs that features a high-affinity tag in the snoRNA and another in a snoRNP core protein. The RNA tag (called U1hpII) is a small (26 nt) stem-loop domain from human U1 snRNA. This structure binds with high affinity (K(D)=10(-11)M) to the RRM domain of the snRNP protein U1A. In our approach, the U1A protein contains a unique affinity tag and is coexpressed in vivo with the tagged snoRNA to yield snoRNP-U1A complexes with two unique protein tags-one in the bound U1A protein and the other in the snoRNP core protein. This scheme has been used effectively to select C/D and H/ACA snoRNPs, including both processing and modifying snoRNPs, and the snoRNA and core proteins are highly enriched. Depending on selection stringency other proteins are isolated as well, including an RNA helicase involved in snoRNP release from pre-rRNA and additional proteins that function in ribosome biogenesis. Tagging the snoRNA component alone is also effective when U1A is expressed with a myc-Tev-protein A fusion sequence. Combined with reduced stringency, enrichment of the U14 snoRNP with this latter system revealed potential interactions with two other snoRNPs, including one processing snoRNP involved in the same cleavages of pre-rRNA.
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106
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Cléry A, Senty-Ségault V, Leclerc F, Raué HA, Branlant C. Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair. Mol Cell Biol 2006; 27:1191-206. [PMID: 17145781 PMCID: PMC1800722 DOI: 10.1128/mcb.01287-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The eukaryal Snu13p/15.5K protein binds K-turn motifs in U4 snRNA and snoRNAs. Two Snu13p/15.5K molecules bind the nucleolar U3 snoRNA required for the early steps of preribosomal processing. Binding of one molecule on the C'/D motif allows association of proteins Nop1p, Nop56p, and Nop58p, whereas binding of the second molecule on the B/C motif allows Rrp9p recruitment. To understand how the Snu13p-Rrp9p pair recognizes the B/C motif, we first improved the identification of RNA determinants required for Snu13p binding by experiments using the systematic evolution of ligands by exponential enrichment. This demonstrated the importance of a U.U pair stacked on the sheared pairs and revealed a direct link between Snu13p affinity and the stability of helices I and II. Sequence and structure requirements for efficient association of Rrp9p on the B/C motif were studied in yeast cells by expression of variant U3 snoRNAs and immunoselection assays. A G-C pair in stem II, a G residue at position 1 in the bulge, and a short stem I were found to be required. The data identify the in vivo function of most of the conserved residues of the U3 snoRNA B/C motif. They bring important information to understand how different K-turn motifs can recruit different sets of proteins after Snu13p association.
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Affiliation(s)
- A Cléry
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France.
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107
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Gagnon KT, Zhang X, Agris PF, Maxwell ES. Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling. J Mol Biol 2006; 362:1025-42. [PMID: 16949610 DOI: 10.1016/j.jmb.2006.07.091] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 07/21/2006] [Accepted: 07/29/2006] [Indexed: 10/24/2022]
Abstract
Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assembly and the resultant changes in sRNA structure or "remodeling" as a consequence of sRNP core protein binding. Hierarchical assembly of the Methanocaldococcus jannaschii sR8 box C/D sRNP is a temperature-dependent process with binding of L7 and Nop56/58 core proteins to the sRNA requiring elevated temperature to facilitate necessary RNA structural dynamics. Circular dichroism (CD) spectroscopy and RNA thermal denaturation revealed an increased order and stability of sRNA folded structure as a result of L7 binding. Subsequent binding of the Nop56/58 and fibrillarin core proteins to the L7-sRNA complex further remodeled sRNA structure. Assessment of sR8 guide region accessibility using complementary RNA oligonucleotide probes revealed significant changes in guide region structure during sRNP assembly. A second dual-guide box C/D sRNA from M. jannaschii, sR6, also exhibited RNA remodeling during temperature-dependent sRNP assembly, although core protein binding was affected by sR6's distinct folded structure. Interestingly, the sR6 sRNP followed an alternative assembly pathway, with both guide regions being continuously exposed during sRNP assembly. Further experiments using sR8 mutants possessing alternative guide regions demonstrated that sRNA folded structure induced by specific guide sequences impacted the sRNP assembly pathway. Nevertheless, assembled sRNPs were active for sRNA-guided methylation independent of the pathway followed. Thus, RNA remodeling appears to be a common and requisite feature of archaeal dual-guide box C/D sRNP assembly and formation of the mature sRNP can follow different assembly pathways in generating catalytically active complexes.
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MESH Headings
- Amino Acid Sequence
- Archaea/chemistry
- Archaea/genetics
- Archaea/metabolism
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/isolation & purification
- Archaeal Proteins/metabolism
- Base Sequence
- Chromatography, Affinity
- Circular Dichroism
- Methylation
- Models, Biological
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Protein Binding
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Temperature
- RNA, Small Untranslated
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Affiliation(s)
- Keith T Gagnon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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108
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Hardin JW, Batey RT. The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity. Nucleic Acids Res 2006; 34:5039-51. [PMID: 16984968 PMCID: PMC1635284 DOI: 10.1093/nar/gkl644] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The archaeal box C/D sRNP, the enzyme responsible for 2'-O-methylation of rRNA and tRNA, possesses a nearly perfect axis of symmetry and bipartite structure. This RNP contains two platforms for the assembly of protein factors, the C/D and C'/D' motifs, acting in conjunction with two guide sequences to direct methylation of a specific 2'-hydroxyl group in a target RNA. While this suggests that a functional asymmetric single-site complex complete with guide sequence and a single box C/D motif should be possible, previous work has demonstrated such constructs are not viable. To understand the basis for a bipartite RNP, we have designed and assayed the activity and specificity of a series of synthetic RNPs that represent a systematic reduction of the wild-type RNP to a fully single-site enzyme. This reduced RNP is active and exhibits all of the characteristics of wild-type box C/D RNPs except it is nonspecific with respect to the site of 2'-O-methylation. Our results demonstrate that protein-protein crosstalk through Nop5p dimerization is not required, but that architecture plays a crucial role in directing methylation activity with both C/D and C'/D' motifs being required for specificity.
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Affiliation(s)
| | - Robert T. Batey
- To whom correspondence should be addressed. Tel: +1 303 735 2159; Fax: +1 303 735 1347;
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109
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Omer AD, Zago M, Chang A, Dennis PP. Probing the structure and function of an archaeal C/D-box methylation guide sRNA. RNA (NEW YORK, N.Y.) 2006; 12:1708-20. [PMID: 16861619 PMCID: PMC1557695 DOI: 10.1261/rna.31506] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Accepted: 05/30/2006] [Indexed: 05/11/2023]
Abstract
The genome of the hyperthermophilic archaeon Sulfolobus solfataricus contains dozens of small C/D-box sRNAs that use a complementary guide sequence to target 2'-O-ribose methylation to specific locations within ribosomal and transfer RNAs. The sRNAs are approximately 50-60 nucleotides in length and contain two RNA structural kink-turn (K-turn) motifs that are required for assembly with ribosomal protein L7Ae, Nop5, and fibrillarin to form an active ribonucleoprotein (RNP) particle. The complex catalyzes guide-directed methylation to target RNAs. Earlier work in our laboratory has characterized the assembly pathway and methylation reaction using the model sR1 sRNA from Sulfolobus acidocaldarius. This sRNA contains only one antisense region situated adjacent to the D-box, and methylation is directed to position U52 in 16S rRNA. Here we have investigated through RNA mutagenesis, the relationship between the sR1 structure and methylation-guide function. We show that although full activity of the guide requires intact C/D and C'/D' K-turn motifs, each structure plays a distinct role in the methylation reaction. The C/D motif is directly implicated in the methylation function, whereas the C'/D' element appears to play an indirect structural role by facilitating the correct folding of the RNA. Our results suggest that L7Ae facilitates the folding of the K-turn motifs (chaperone function) and, in addition, is required for methylation activity in the presence of Nop5 and Fib.
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Affiliation(s)
- Arina D Omer
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.
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110
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Schultz A, Nottrott S, Watkins NJ, Lührmann R. Protein-protein and protein-RNA contacts both contribute to the 15.5K-mediated assembly of the U4/U6 snRNP and the box C/D snoRNPs. Mol Cell Biol 2006; 26:5146-54. [PMID: 16782898 PMCID: PMC1489164 DOI: 10.1128/mcb.02374-05] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The k-turn-binding protein 15.5K is unique in that it is essential for the hierarchical assembly of three RNP complexes distinct in both composition and function, namely, the U4/U6 snRNP, the box C/D snoRNP, and the RNP complex assembled on the U3 box B/C motif. 15.5K interacts with the cognate RNAs via an induced fit mechanism, which results in the folding of the surrounding RNA to create a binding site(s) for the RNP-specific proteins. However, it is possible that 15.5K also mediates RNP formation via protein-protein interactions with the complex-specific proteins. To investigate this possibility, we created a series of 15.5K mutations in which the surface properties of the protein had been changed. We assessed their ability to support the formation of the three distinct RNP complexes and found that the formation of each RNP requires a distinct set of regions on the surface of 15.5K. This implies that protein-protein contacts are essential for RNP formation in each complex. Further supporting this idea, direct protein-protein interaction could be observed between hU3-55K and 15.5K. In conclusion, our data suggest that the formation of each RNP involves the direct recognition of specific elements in both 15.5K protein and the specific RNA.
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Affiliation(s)
- Annemarie Schultz
- Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, D-37070 Göttingen, Germany
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111
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Zhang X, Champion EA, Tran EJ, Brown BA, Baserga SJ, Maxwell ES. The coiled-coil domain of the Nop56/58 core protein is dispensable for sRNP assembly but is critical for archaeal box C/D sRNP-guided nucleotide methylation. RNA (NEW YORK, N.Y.) 2006; 12:1092-103. [PMID: 16601205 PMCID: PMC1464844 DOI: 10.1261/rna.2230106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Archaeal box C/D sRNAs guide the methylation of specific nucleotides in archaeal ribosomal and tRNAs. Three Methanocaldococcus jannaschii sRNP core proteins (ribosomal protein L7, Nop56/58, and fibrillarin) bind the box C/D sRNAs to assemble the sRNP complex, and these core proteins are essential for nucleotide methylation. A distinguishing feature of the Nop56/58 core protein is the coiled-coil domain, established by alpha-helices 4 and 5, that facilitates Nop56/58 self-dimerization in vitro. The function of this coiled-coil domain has been assessed for box C/D sRNP assembly, sRNP structure, and sRNP-guided nucleotide methylation by mutating or deleting this protein domain. Protein pull-down experiments demonstrated that Nop56/58 self-dimerization and Nop56/58 dimerization with the core protein fibrillarin are mutually exclusive protein:protein interactions. Disruption of Nop56/58 homodimerization by alteration of specific amino acids or deletion of the entire coiled-coil domain had no obvious effect upon core protein binding and sRNP assembly. Site-directed mutation of the Nop56/58 homodimerization domain also had no apparent effect upon either box C/D RNP- or C'/D' RNP-guided nucleotide modification. However, deletion of this domain disrupted guided methylation from both RNP complexes. Nuclease probing of the sRNP assembled with Nop56/58 proteins mutated in the coiled-coil domain indicated that while functional complexes were assembled, box C/D and C'/D' RNPs were altered in structure. Collectively, these experiments revealed that the self-dimerization of the Nop56/58 coiled-coil domain is not required for assembly of a functional sRNP, but the coiled-coil domain is important for the establishment of wild-type box C/D and C'/D' RNP structure essential for nucleotide methylation.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Crystallography, X-Ray
- Dimerization
- Methylation
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Nucleotides/metabolism
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Sequence Alignment
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Affiliation(s)
- Xinxin Zhang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, 27695, USA
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112
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Russell AG, Schnare MN, Gray MW. A Large Collection of Compact Box C/D snoRNAs and their Isoforms in Euglena gracilis: Structural, Functional and Evolutionary Insights. J Mol Biol 2006; 357:1548-65. [PMID: 16497322 DOI: 10.1016/j.jmb.2006.01.063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 01/10/2006] [Accepted: 01/17/2006] [Indexed: 11/27/2022]
Abstract
In the domains Eucarya and Archaea, box C/D RNAs guide methylation at the 2'-position of selected ribose residues in ribosomal RNA (rRNA). Those eukaryotic box C/D RNAs that have been identified to date are larger and more variable in size than their archaeal counterparts. Here, we report the first extensive identification and characterization of box C/D small nucleolar (sno) RNAs from the protist Euglena gracilis. Among several unexpected findings, this organism contains a large assortment of methylation-guide RNAs that are smaller and more uniformly sized than those of other eukaryotes, and that consist of surprisingly few double-guide RNAs targeting sites of rRNA modification. Our comprehensive examination of the modification status of E.gracilis rRNA indicates that many of these box C/D snoRNAs target clustered methylation sites requiring extensive, overlapping guide RNA/rRNA pairings. An examination of the structure of the RNAs, in particular the location of the functional guide elements, suggests that the distances between adjacent box elements are an important factor in determining which of the potential guide elements is used to target a site of O(2')-methylation.
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Affiliation(s)
- Anthony G Russell
- Department of Biochemistry and Molecular Biology Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5.
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113
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Nolivos S, Carpousis AJ, Clouet-d'Orval B. The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn. Nucleic Acids Res 2005; 33:6507-14. [PMID: 16293637 PMCID: PMC1289080 DOI: 10.1093/nar/gki962] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 10/29/2005] [Accepted: 10/29/2005] [Indexed: 12/03/2022] Open
Abstract
The C/D guide RNAs predicted from the genomic sequences of three species of Pyrococcus delineate a family of small non-coding archaeal RNAs involved in the methylation of rRNA and tRNA. The C/D guides assemble into ribonucleoprotein (RNP) that contains the methyltransferase. The protein L7Ae, a key structural component of the RNP, binds to a Kink-turn (K-turn) formed by the C/D motif. The K-turn is a structure that consists of two RNA stems separated by a short asymmetric loop with a characteristic sharp bend (kink) between the two stems. The majority of the pyrococcal C/D guides contain a short 3 nt-spacer between the C'/D' motifs. We show here that conserved terminal stem-loops formed by the C'/D' motif of the Pyrococcus C/D RNAs are also L7Ae-binding sites. These stem-loops are related to the K-turn by sequence and structure, but they consist of a single stem closed by a terminal loop. We have named this structure the K-loop. We show that conserved non-canonical base pairs in the stem of the K-loop are necessary for L7Ae binding. For the C/D guides with a 3 nt-spacer we show that the sequence and length is also important. The K-loop could improve the stability of the C/D guide RNAs in Pyrococcal species, which are extreme hyperthermophiles.
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Affiliation(s)
- Sophie Nolivos
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, UMR 5100 Université Paul Sabatier118 route de Narbonne, 31062 Toulouse cedex 9, France
| | - Agamemnon J. Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, UMR 5100 Université Paul Sabatier118 route de Narbonne, 31062 Toulouse cedex 9, France
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, UMR 5100 Université Paul Sabatier118 route de Narbonne, 31062 Toulouse cedex 9, France
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114
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Dennis PP, Omer A. Small non-coding RNAs in Archaea. Curr Opin Microbiol 2005; 8:685-94. [PMID: 16256421 DOI: 10.1016/j.mib.2005.10.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 10/12/2005] [Indexed: 10/25/2022]
Abstract
Biochemical and informatics analyses conducted over the past few years have revealed the presence of a plethora of small non-coding RNAs in various species of Archaea. A large proportion of these RNAs contain a common structural motif called the RNA kink turn (K-turn). The best-characterized are the C/D box and the H/ACA box guide small (s)RNAs. Both contain the K-turn fold and require the binding of the L7Ae protein to stabilize the structure of this crucial motif. These sRNAs assemble with L7Ae and several other proteins into complex and dynamic ribonucleoprotein machines that mediate guide-directed ribose methylation or pseudouridylation to specific locations in ribosomal or transfer RNA. Analyses of new archaeal sRNA libraries have identified additional classes of novel sRNAs; many of these contain the RNA K-turn motif and suggest that the RNAs might function as ribonucleoprotein complexes. Some have characteristics of small interfering RNAs or of micro RNAs that have been implicated in the post-transcriptional control of gene expression, whereas others appear to be involved in protein translocation or in ribosomal RNA processing and ribosome assembly. A complete understanding of the structure of the K-turn motif and its contribution to various RNA-RNA and RNA-protein interactions will be absolutely essential to fully elucidate the biological organization, activity and function of these novel archaeal ribonucleoprotein machines.
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Affiliation(s)
- Patrick P Dennis
- The Division of Molecular and Cellular Biosciences, National Science Foundation, 4201 Wilson Blvd., Arlington, VA 22230, USA
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115
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Yang H, Henning D, Valdez BC. Functional interaction between RNA helicase II/Gu(alpha) and ribosomal protein L4. FEBS J 2005; 272:3788-802. [PMID: 16045751 DOI: 10.1111/j.1742-4658.2005.04811.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA helicase II/Gu(alpha) is a multifunctional nucleolar protein involved in ribosomal RNA processing in Xenopus laevis oocytes and mammalian cells. Downregulation of Gu(alpha) using small interfering RNA (siRNA) in HeLa cells resulted in 80% inhibition of both 18S and 28S rRNA production. The mechanisms underlying this effect remain unclear. Here we show that in mammalian cells, Gu(alpha) physically interacts with ribosomal protein L4 (RPL4), a component of 60S ribosome large subunit. The ATPase activity of Gu(alpha) is important for this interaction and is also necessary for the function of Gu(alpha) in the production of both 18S and 28S rRNAs. Knocking down RPL4 expression using siRNA in mouse LAP3 cells inhibits the production of 47/45S, 32S, 28S, and 18S rRNAs. This inhibition is reversed by exogenous expression of wild-type human RPL4 protein but not the mutant form lacking Gu(alpha)-interacting motif. These observations have suggested that the function of Gu(alpha) in rRNA processing is at least partially dependent on its ability to interact with RPL4.
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Affiliation(s)
- Hushan Yang
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
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116
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Szewczak LBW, Gabrielsen JS, Degregorio SJ, Strobel SA, Steitz JA. Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein. RNA (NEW YORK, N.Y.) 2005; 11:1407-19. [PMID: 16120832 PMCID: PMC1370824 DOI: 10.1261/rna.2830905] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Accepted: 05/31/2005] [Indexed: 05/04/2023]
Abstract
The interaction between box C/D small nucleolar (sno)RNAs and the 15.5K protein nucleates snoRNP assembly. Many eukaryotic snoRNAs contain two potential binding sites for this protein, only one of which appears to be utilized in vivo. The binding site conforms to the consensus for a kink-turn motif. We have investigated the molecular basis for selection of one potential site over the other using in vitro mobility shift assays and nucleotide analog interference mapping of Xenopus U25 snoRNA and of a circularly permuted form. We find that preferential binding of human 15.5K is not dependent on the proximity of RNA ends, but instead appears to require a structural context beyond the kink-turn itself. Direct analysis of the energetic contributions to binding made by 18 functional groups within the kink-turn identified both backbone atoms and base functionalities as key for interaction. An intramolecular RNA-RNA contact via a 2'-hydroxyl may supercede a putative Type I A-minor interaction in stabilizing the RNA-protein complex.
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117
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Ziesche SM, Omer AD, Dennis PP. RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea. Mol Microbiol 2005; 54:980-93. [PMID: 15522081 DOI: 10.1111/j.1365-2958.2004.04319.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Archaea use ribonucleoprotein (RNP) machines similar to those found in the eukaryotic nucleolus to methylate ribose residues in nascent ribosomal RNA. The archaeal complex required for this 2'-O-ribose-methylation consists of the C/D box sRNA guide and three proteins, the core RNA-binding aL7a protein, the aNop56 protein and the methyltransferase aFib protein. These RNP machines were reconstituted in vitro from purified recombinant components, and shown to have methylation activity when provided with a simple target oligonucleotide, complementary to the sRNA guide sequence. To obtain a better understanding of the versatility and specificity of this reaction, the activity of reconstituted particles on more complex target substrates, including 5S RNA, tRNA(Gln) and 'double target' oligonucleotides that exhibit either direct or reverse complementarity to both the D' and D box guides, has been examined. The natural 5S and tRNA(Gln) substrates were efficiently methylated in vitro, as long as the complementarity between guide and target was about 10 base pairs in length, and lacked mismatches. Maximal activity of double guide sRNAs required that both methylation sites be present in cis on the target RNA.
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Affiliation(s)
- Sonia M Ziesche
- Department of Biochemistry and Molecular Biology University of British Columbia 2146 Health Sciences Mall Vancouver, BC, V6T 1Z3, Canada
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118
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Ballarino M, Morlando M, Pagano F, Fatica A, Bozzoni I. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae. Mol Cell Biol 2005; 25:5396-403. [PMID: 15964797 PMCID: PMC1156983 DOI: 10.1128/mcb.25.13.5396-5403.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carboxy-terminal domain (CTD) of RNA polymerase II large subunit acts as a platform to assemble the RNA processing machinery in a controlled way throughout the transcription cycle. In yeast, recent findings revealed a physical connection between phospho-CTD, generated by the Ctk1p kinase, and protein factors having a function in small nucleolar RNA (snoRNA) biogenesis. The snoRNAs represent a large family of polymerase II noncoding transcripts that are associated with highly conserved polypeptides to form stable ribonucleoprotein particles (snoRNPs). In this work, we have studied the biogenesis of the snoRNPs belonging to the box H/ACA class. We report that the assembly factor Naf1p and the core components Cbf5p and Nhp2p are recruited on H/ACA snoRNA genes very early during transcription. We also show that the cotranscriptional recruitment of Naf1p and Cbf5p is Ctk1p dependent and that Ctk1p and Cbf5p are required for preventing the readthrough into the snoRNA downstream genes. All these data suggest that proper cotranscriptional snoRNP assembly controls 3'-end formation of snoRNAs and, consequently, the release of a functional particle.
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Affiliation(s)
- Monica Ballarino
- Institute Pasteur Fondazione Cenci-Bolognetti, Department of Genetics and Molecular Biology, University La Sapienza, P.le A. Moro 5, 00185 Rome, Italy
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119
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Zago MA, Dennis PP, Omer AD. The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 2005; 55:1812-28. [PMID: 15752202 DOI: 10.1111/j.1365-2958.2005.04505.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Archaeal L7Ae is a multifunctional protein that binds to a distinctive K-turn motif in RNA and is found as a component in the large subunit of the ribosome, and in ribose methylation and pseudouridylation guide RNP particles. A collection of L7Ae-associated small RNAs were isolated from Sulfolobus solfataricus cell extracts and used to construct a cDNA library; 45 distinct cDNA sequences were characterized and divided into six groups. Group 1 contained six RNAs that exhibited the features characteristic of the canonical C/D box archaeal sRNAs, two RNAs that were atypical C/D box sRNAs and one RNA representative of archaeal H/ACA sRNA family. Group 2 contained 13 sense strand RNA sequences that were encoded either within, or overlapping annotated open reading frames (ORFs). Group 3 contained three sequences form intergenic regions. Group 4 contained antisense sequences from within or overlapping sense strand ORFs or antisense sequences to C/D box sRNAs. More than two-thirds of these sequences possessed K-turn motifs. Group 5 contained two sequences corresponding to internal regions of 7S RNA. Group 6 consisted of 11 sequences that were fragments from the 5' or 3' ends of 16S and 23S ribosomal RNA and from seven different tRNAs. Our data suggest that S. solfataricus contains a plethora of small RNAs. Most of these are bound directly by the L7Ae protein; the others may well be part of larger, transiently stable RNP complexes that contain the L7Ae protein as core component.
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MESH Headings
- Base Sequence
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Complementary
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/isolation & purification
- RNA, Archaeal/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/isolation & purification
- RNA, Untranslated/metabolism
- RNA-Binding Proteins/chemistry
- Ribonucleoproteins/chemistry
- Ribosomal Proteins/chemistry
- Sequence Analysis, DNA
- Sulfolobus solfataricus/chemistry
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Affiliation(s)
- Maria A Zago
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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120
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Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA (NEW YORK, N.Y.) 2005; 11:1051-63. [PMID: 15987815 PMCID: PMC1370790 DOI: 10.1261/rna.2110805] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We identified the first archaeal tRNA ribose 2'-O-methylase, aTrm56, belonging to the Cluster of Orthologous Groups (COG) 1303 that contains archaeal genes only. The corresponding protein exhibits a SPOUT S-adenosylmethionine (AdoMet)-dependent methyltransferase domain found in bacterial and yeast G18 tRNA 2'-O-methylases (SpoU, Trm3). We cloned the Pyrococcus abyssi PAB1040 gene belonging to this COG, expressed and purified the corresponding protein, and showed that in vitro, it specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of C at position 56 in tRNA transcripts. This tRNA methylation is present only in archaea, and the gene for this enzyme is present in all the archaeal genomes sequenced up to now, except in the crenarchaeon Pyrobaculum aerophilum. In this archaea, the C56 2'-O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs.
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MESH Headings
- Amino Acid Sequence
- Catalysis
- Cloning, Molecular
- Consensus Sequence
- Cytosine/metabolism
- Escherichia coli/genetics
- Genome, Archaeal
- Glutathione Transferase/metabolism
- Kinetics
- Molecular Sequence Data
- Molecular Weight
- Open Reading Frames
- Phylogeny
- Protein Structure, Secondary
- Pyrobaculum/genetics
- Pyrobaculum/metabolism
- Pyrococcus abyssi/enzymology
- Pyrococcus abyssi/genetics
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Sequence Homology, Amino Acid
- Substrate Specificity
- Temperature
- tRNA Methyltransferases/chemistry
- tRNA Methyltransferases/classification
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Marie-Hélène Renalier
- IEFG 109, Laboratoire de Biologie Moléculaire des Eucaryotes, (LBME) UMR CNRS/UHP 5099 118, route de Narbonne, 31062 Toulouse Cedex 02, France
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121
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Charpentier B, Muller S, Branlant C. Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation. Nucleic Acids Res 2005; 33:3133-44. [PMID: 15933208 PMCID: PMC1142404 DOI: 10.1093/nar/gki630] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Pseudouridine (Ψ) are frequently modified residues in RNA. In Eukarya, their formation is catalyzed by enzymes or by ribonucleoprotein complexes (RNPs) containing H/ACA snoRNAs. H/ACA sRNA and putative ORFs for H/ACA sRNP proteins (L7Ae, aCBF5, aNOP10 and aGAR1) were found in Archaea. Here, by using Pyrococcus abyssi recombinant proteins and an in vitro transcribed P.abyssi H/ACA sRNA, we obtained the first complete in vitro reconstitution of an active H/ACA RNP. Both L7Ae and the aCBF5 RNA:Ψ synthase bind directly the sRNA; aCBF5 also interacts directly and independently with aNOP10 and aGAR1. Presence of aCBF5, aNOP10 and a U residue at the pseudouridylation site in the target RNA are required for RNA target recruitment. In agreement, we found that the aCBF5–aNOP10 pair is the minimal set of proteins needed for the formation of a particle active for pseudouridylation. However, particles more efficient in targeted pseudouridylation can be formed with the addition of proteins L7Ae and/or aGAR1. Although necessary for optimal activity, the conserved ACA motif in the sRNA was found to be not essential.
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Affiliation(s)
- Bruno Charpentier
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 UHP-CNRS, Université des Sciences et Techniques Henri Poincaré Nancy I 54506 Vandoeuvre-Lès-Nancy cedex, France.
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122
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Russell AG, Watanabe YI, Charette JM, Gray MW. Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya. Nucleic Acids Res 2005; 33:2781-91. [PMID: 15894796 PMCID: PMC1126904 DOI: 10.1093/nar/gki574] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Box C/D ribonucleoprotein (RNP) particles mediate O2′-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts, containing four core protein components (Snu13p, Nop56p, Nop58p and fibrillarin) compared with three in Archaea. This increase in complexity raises questions about the evolutionary emergence of the eukaryote-specific proteins and structural conservation in these RNPs throughout the eukaryotic domain. In protists, the primarily unicellular organisms comprising the bulk of eukaryotic diversity, the protein composition of box C/D RNPs has not yet been extensively explored. This study describes the complete gene, cDNA and protein sequences of the fibrillarin homolog from the protozoon Euglena gracilis, the first such information to be obtained for a nucleolus-localized protein in this organism. The E.gracilis fibrillarin gene contains a mixture of intron types exhibiting markedly different sizes. In contrast to most other E.gracilis mRNAs characterized to date, the fibrillarin mRNA lacks a spliced leader (SL) sequence. The predicted fibrillarin protein sequence itself is unusual in that it contains a glycine-lysine (GK)-rich domain at its N-terminus rather than the glycine-arginine-rich (GAR) domain found in most other eukaryotic fibrillarins. In an evolutionarily diverse collection of protists that includes E.gracilis, we have also identified putative homologs of the other core protein components of box C/D RNPs, thereby providing evidence that the protein composition seen in the higher eukaryotic complexes was established very early in eukaryotic cell evolution.
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Affiliation(s)
- Anthony G Russell
- Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia, Canada B3H 1X5.
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123
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Baker DL, Youssef OA, Chastkofsky MIR, Dy DA, Terns RM, Terns MP. RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. Genes Dev 2005; 19:1238-48. [PMID: 15870259 PMCID: PMC1132009 DOI: 10.1101/gad.1309605] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotes and archaea, uridines in various RNAs are converted to pseudouridines by RNA-guided RNA modification complexes termed H/ACA RNPs. Guide RNAs within the complexes base-pair with target RNAs to direct modification of specific ribonucleotides. Cbf5, a protein component of the complex, likely catalyzes the modification. However, little is known about the organization of H/ACA RNPs and the roles of the multiple proteins thought to comprise the complexes. We have reconstituted functional archaeal H/ACA RNPs from recombinant components, defined the components necessary and sufficient for function, and determined the direct RNA-protein and protein-protein interactions that occur between the components. The results provide substantial insight into the functional organization of this RNP. The functional complex requires a guide RNA and each of four proteins: Cbf5, Gar1, L7Ae, and Nop10. Two proteins interact directly with the guide RNA: L7Ae and Cbf5. L7Ae does not interact with other H/ACA RNP proteins in the absence of the RNA. We have defined two novel functions for Cbf5. Cbf5 is the protein that specifically recognizes and binds H/ACA guide RNAs. In addition, Cbf5 recruits the two other essential proteins, Gar1 and Nop10, to the pseudouridylation guide complex.
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Affiliation(s)
- Daniel L Baker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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124
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Tang TH, Polacek N, Zywicki M, Huber H, Brugger K, Garrett R, Bachellerie JP, Hüttenhofer A. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol Microbiol 2005; 55:469-81. [PMID: 15659164 DOI: 10.1111/j.1365-2958.2004.04428.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
By generating a specialized cDNA library from the archaeon Sulfolobus solfataricus, we have identified 57 novel small non-coding RNA (ncRNA) candidates and confirmed their expression by Northern blot analysis. The majority was found to belong to one of two classes, either antisense or antisense-box RNAs, where the latter only exhibit partial complementarity to RNA targets. The most prominent group of antisense RNAs is transcribed in the opposite orientation to the transposase genes, encoded by insertion elements (transposons). Thus, these antisense RNAs may regulate transposition of insertion elements by inhibiting expression of the transposase mRNA. Surprisingly, the class of antisense RNAs also contained RNAs complementary to tRNAs or sRNAs (small-nucleolar-like RNAs). For the antisense-box ncRNAs, the majority could be assigned to the class of C/D sRNAs, which specify 2'-O-methylation sites on rRNAs or tRNAs. Five C/D sRNAs of this group are predicted to target methylation at six sites in 13 different tRNAs, thus pointing to the widespread role of these sRNA species in tRNA modification in Archaea. Another group of antisense-box RNAs, lacking typical C/D sRNA motifs, was predicted to target the 3'-untranslated regions of certain mRNAs. Furthermore, one of the ncRNAs that does not show antisense elements is transcribed from a repeat unit of a cluster of small regularly spaced repeats in S. solfataricus which is potentially involved in replicon partitioning. In conclusion, this is the first report of stably expressed antisense RNAs in an archaeal species and it raises the prospect that antisense-based mechanisms are also used widely in Archaea to regulate gene expression.
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Affiliation(s)
- Thean-Hock Tang
- Institute for Research in Molecular Medicine, University Sains Malaysia Health Campus, 16150 Kubang Kerian, Kelatan, Malaysia
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125
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Clouet-d'Orval B, Gaspin C, Mougin A. Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. Biochimie 2005; 87:889-95. [PMID: 16164996 DOI: 10.1016/j.biochi.2005.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Accepted: 02/10/2005] [Indexed: 10/25/2022]
Abstract
The biogenesis of tRNA involves multiple reactions including post-transcriptional modifications and pre-tRNA splicing. Among the three domains of life, only Archaea have two different mechanisms for tRNA ribose methylation: site-specific 2'-O-methyltransferases and C/D guided-RNA machinery. Recently, the first archaeal tRNA 2'-O-methyltransferase, aTrm56, has been characterized. This enzyme is found in all archaeal genomes sequenced so far except one and belongs to the SPOUT family (class IV) of RNA methyltransferases. Its substrate is the conserved C56 in the T-loop of archaeal tRNAs. In the crenarchaeon Pyrobaculum aerophylum, in which no homologue of this methyltransferase is found, a box C/D guide sRNP insures the ribose methylation of C56. Moreover, a new twist on tRNA processing is the finding, in most euryarchaeal tRNAtrp genes, of a box C/D guide RNA within their intron specifying methylation at two sites. Modification of tRNA is an integral part of the complex maturation process of primary tRNA transcripts. In addition to their role in modification, both modification enzymes and C/D guide RNPs may have a chaperone function insuring the precise folding of the mature, functional tRNA.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie Génétique et Moléculaire, UMR5100 Université Paul-Sabatier, 118, route de Narbonne, 31062 Toulouse, France.
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126
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Abstract
The cell nucleolus is the subnuclear body in which ribosomal subunits are assembled, and it is also the location of several processes not related to ribosome biogenesis. Recent studies have revealed that nucleolar components move about in a variety of ways. One class of movement is associated with ribosome assembly, which is a vectorial process originating at the sites of transcription in the border region between the fibrillar center and the dense fibrillar component. The nascent preribosomal particles move outwardly to become the granular components where further maturation takes place. These particles continue their travel through the nucleoplasm for eventual export to the cytoplasm to become functional ribosomes. In a second kind of motion, many nucleolar components rapidly exchange with the nucleoplasm. Thirdly, nucleolar components engage in very complex movements when the nucleolus disassembles at the beginning of mitosis and then reassembles at the end of mitosis. Finally, many other cellular and viral macromolecules, which are not related to ribosome assembly, also pass through or are retained by the nucleolus. These are involved in nontraditional roles of the nucleolus, including regulation of tumor suppressor and oncogene activities, signal recognition particle assembly, modification of small RNAs, control of aging, and modulating telomerase function.
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Affiliation(s)
- M O J Olson
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216, USA.
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127
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Tran E, Zhang X, Lackey L, Maxwell ES. Conserved spacing between the box C/D and C'/D' RNPs of the archaeal box C/D sRNP complex is required for efficient 2'-O-methylation of target RNAs. RNA (NEW YORK, N.Y.) 2005; 11:285-93. [PMID: 15661846 PMCID: PMC1370718 DOI: 10.1261/rna.7223405] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Accepted: 12/03/2004] [Indexed: 05/24/2023]
Abstract
RNA-guided nucleotide modification complexes direct the post-transcriptional nucleotide modification of both archaeal and eukaryotic RNAs. We have previously demonstrated that efficient 2'-O-methylation activity guided by an in vitro reconstituted archaeal box C/D sRNP requires juxtaposed box C/D and C'/D' RNP complexes. In these experiments, we investigate the importance of spatially positioning the box C/D and C'/D' RNPs within the sRNP complex for nucleotide modification. Initial sequence analysis of 245 archaeal box C/D sRNAs from both Eukyarchaeota and Crenarchaeota kingdoms revealed highly conserved spacing between the box C/D and C'/D' RNA motifs. Distances between boxes C to D' and C' to D (D' and D spacers, respectively) exhibit highly constrained lengths of 12 nucleotides (nt). Methanocaldococcus jannaschii sR8 sRNA, a model box C/D sRNA with D and D' spacers of 12 nt, was mutated to alter the distance between the two RNA motifs. sRNAs with longer or shorter spacer regions could still form sRNPs by associating with box C/D core proteins, L7, Nop56/58, and fibrillarin, comparable to wild-type sR8. However, these reconstituted box C/D sRNP complexes were severely deficient in methylation activity. Alteration of the D and D' spacer lengths disrupted the guided methylation activity of both the box C/D and C'/D' RNP complexes. When only one spacer region was altered, methylation activity of the corresponding RNP was lost. Collectively, these results demonstrate the importance of box C/D and C'/D' RNP positioning for preservation of critical inter-RNP interactions required for efficient box C/D sRNP-guided nucleotide methylation.
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Affiliation(s)
- Elizabeth Tran
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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128
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Abstract
From archaea to humans, C/D- and H/ACA-type small ribonucleoprotein particles play key roles in crucial RNA processing events. Various such particles are required for pre-rRNA cleavage steps and/or for chemical modification of rRNAs, spliceosomal small nuclear RNAs, tRNAs and perhaps even mRNAs. Each C/D-type particle contains a small RNA possessing conserved C and D, as well as related C' and D', sequence motifs, whereas each H/ACA-type particle contains a small RNA featuring conserved H and ACA sequence elements. Recently published studies highlight the importance of sequence and structural elements of these RNAs in the localization, activity and assembly of the ribonucleoprotein particles. A novel sequence element, the Cajal body box, found at the apex of stem structures within a subset of H/ACA small RNAs, mediates the specific retention of particles containing these elements inside nucleoplasmic Cajal bodies. Two highly conserved elements, the m1 and m2 boxes, have been identified in the 3' stem of the atypical H/ACA snR30/U17 RNAs. These conserved sequence elements are necessary for early pre-rRNA cleavage events and consequently for mature 18S rRNA production. Finally, convincing evidence has been provided that the conserved C and D sequence motifs of C/D-type small RNAs fold into a helix-bulge-helix structure, called a kink-turn, that provides a platform for assembly of C/D-type ribonucleoprotein particles.
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Affiliation(s)
- Anthony K Henras
- Department of Chemistry & Biochemistry, UCLA Box 951569, 607 Charles E Young Drive East, Los Angeles, CA 90095-1569, USA
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129
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Mechanisms and functions of RNA-guided RNA modification. FINE-TUNING OF RNA FUNCTIONS BY MODIFICATION AND EDITING 2004. [DOI: 10.1007/b105585] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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130
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Tran E, Brown J, Maxwell ES. Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus? Trends Biochem Sci 2004; 29:343-50. [PMID: 15236741 DOI: 10.1016/j.tibs.2004.05.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Elizabeth Tran
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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131
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Henras AK, Capeyrou R, Henry Y, Caizergues-Ferrer M. Cbf5p, the putative pseudouridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs. RNA (NEW YORK, N.Y.) 2004; 10:1704-12. [PMID: 15388873 PMCID: PMC1370658 DOI: 10.1261/rna.7770604] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Box C/D and box H/ACA small ribonucleoprotein particles (sRNPs) are found from archaea to humans, and some of these play key roles during the biogenesis of ribosomes or components of the splicing apparatus. The protein composition of the core of both types of particles is well established and the assembly pathway of box C/D sRNPs has been extensively investigated both in archaeal and eukaryotic systems. In contrast, knowledge concerning the mode of assembly and final structure of box H/ACA sRNPs is much more limited. In the present study, we have investigated the protein/protein interactions taking place between the four protein components of yeast box H/ACA small nucleolar RNPs (snoRNPs), Cbf5p, Gar1p, Nhp2p, and Nop10p. We provide evidence that Cbf5p, Gar1p, and Nop10p can form a complex devoid of Nhp2p and small nucleolar RNA (snoRNA) components of the particles and that Cbf5p and Nop10p can directly bind to each other. We also show that the absence of any component necessary for assembly of box H/ACA snoRNPs inhibits accumulation of Cbf5p, Gar1p, or Nop10p, whereas Nhp2p levels are little affected.
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS and Université Paul Sabatier, IFR109, 118 route de Narbonne, 31062 Toulouse cedex 04, France, European Union
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132
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Charron C, Manival X, Cléry A, Senty-Ségault V, Charpentier B, Marmier-Gourrier N, Branlant C, Aubry A. The archaeal sRNA binding protein L7Ae has a 3D structure very similar to that of its eukaryal counterpart while having a broader RNA-binding specificity. J Mol Biol 2004; 342:757-73. [PMID: 15342235 DOI: 10.1016/j.jmb.2004.07.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 07/10/2004] [Accepted: 07/12/2004] [Indexed: 11/26/2022]
Abstract
The ribosomal L7Ae protein of archaea has the peculiarity to be a component of the C/D and H/ACA snRNPs, that guide rRNA post-transcriptional modifications. Its yeast (Snu13p) and human (15.5kDa protein) homologs are only found in C/D snoRNPs and the (U4/U6, U5) spliceosomal tri-snRNP. By using a large variety of RNAs, we compared the RNA-binding specificities of the recombinant Pyrococcus abyssi L7Ae and Saccharomyces cerevisiae Snu13 proteins. Unlike Snu13p, protein L7Ae binds terminal loops closed by two A:G and G:A pairs and canonical K-turn structures with similar efficiencies, provided that the terminal loop contains at least 5nt. In contrast to Snu13p, binding of protein L7Ae to canonical K-turn structures is not dependent on the identity of the residue at position 2 in the bulge. The peculiar KT-15 motif of P. abyssi 23S rRNA, that is recognized by L7Ae, does not associate with Snu13p. To get more information on the P. abyssi L7Ae protein, we solved its X-ray structure at 1.9A resolution. In spite of their sequence divergence, the free P. abyssi and bound H. marismortui proteins were found to have highly similar structures. Only a limited number of side-chain conformational changes occur at the protein-RNA interface upon RNA binding. In particular, one ion pair that is formed by residues Glu43 and Lys46 in the free protein is disrupted in the ribosomal 50S subunit, so that, residue Glu43 can interact with the RNA residue G264. The Glu43-Lys46 ion pair of protein L7Ae belongs to a complex network of ion pairs that may participate to protein thermostability.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Base Sequence
- Binding Sites
- Haloarcula marismortui/genetics
- Haloarcula marismortui/metabolism
- Humans
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- Pyrococcus abyssi/genetics
- Pyrococcus abyssi/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Static Electricity
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Affiliation(s)
- C Charron
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, UMR CNRS 7036, Groupe Biocristallographie, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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133
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Aittaleb M, Visone T, Fenley MO, Li H. Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin. J Biol Chem 2004; 279:41822-9. [PMID: 15286083 DOI: 10.1074/jbc.m406209200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Archaea, fibrillarin and Nop5p form the core complex of box C/D small ribonucleoprotein particles, which are responsible for site-specific 2'-hydroxyl methylation of ribosomal and transfer RNAs. Fibrillarin has a conserved methyltransferase fold and employs S-adenosyl-l-methionine (AdoMet) as the cofactor in methyl transfer reactions. Comparison between recently determined crystal structures of free fibrillarin and fibrillarin-Nop5p-AdoMet tertiary complex revealed large conformational differences at the cofactor-binding site in fibrillarin. To identify the structural elements responsible for these large conformational differences, we refined a crystal structure of Archaeoglobus fulgidus fibrillarin-Nop5p binary complex at 3.5 A. This structure exhibited a pre-formed backbone geometry at the cofactor binding site similar to that when the cofactor is bound, suggesting that binding of Nop5p alone to fibrillarin is sufficient to stabilize the AdoMet-binding pocket. Calorimetry studies of cofactor binding to fibrillarin alone and to fibrillarin-Nop5p binary complex provided further support for this role of Nop5p. Mutagenesis and thermodynamic data showed that a cation-pi bridge formed between Tyr-89 of fibrillarin and Arg-169 of Nop5p, although dispensable for in vitro methylation activity, could partially account for the enhanced binding of cofactor to fibrillarin by Nop5p. Finally, assessment of cofactor-binding thermodynamics and catalytic activities of enzyme mutants identified three additional fibrillarin residues (Thr-70, Glu-88, and Asp-133) to be important for cofactor binding and for catalysis.
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Affiliation(s)
- Mohamed Aittaleb
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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134
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Starostina NG, Marshburn S, Johnson LS, Eddy SR, Terns RM, Terns MP. Circular box C/D RNAs in Pyrococcus furiosus. Proc Natl Acad Sci U S A 2004; 101:14097-101. [PMID: 15375211 PMCID: PMC521125 DOI: 10.1073/pnas.0403520101] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Box C/D RNAs are small, noncoding RNAs that function in RNA modification in eukaryotes and archaea. Here, we report that box C/D RNAs exist in the rare biological form of RNA circles in the hyperthermophilic archaeon Pyrococcus furiosus. Northern analysis of box C/D RNAs reveals two prominent RNA species of different electrophoretic mobilities in total P. furiosus RNA preparations. Together, the results of Northern, ribozyme, RT-PCR, and lariat debranching analyses indicate that the two species are circular and linear RNAs of similar length and abundance. It seems that most, if not all, species of box C/D RNAs exist as circles in P. furiosus. In addition, the circular RNAs are found in complexes with proteins required for box C/D RNA function. Our finding places box C/D RNAs among the extremely few circular RNAs known to exist in nature. Moreover, the unexpected discovery of circular box C/D RNAs points to the existence of a previously unrecognized biogenesis pathway for box C/D RNAs in archaea.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Western
- Conserved Sequence
- Immunoprecipitation/methods
- Molecular Sequence Data
- Nucleic Acid Conformation
- Pyrococcus furiosus/chemistry
- Pyrococcus furiosus/genetics
- RNA/genetics
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Catalytic/analysis
- RNA, Catalytic/genetics
- RNA, Circular
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Rabbits
- Recombinant Proteins/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins, Small Nucleolar/genetics
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Affiliation(s)
- Natalia G Starostina
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Science Building, Athens, GA 30602, USA
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135
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Singh SK, Gurha P, Tran EJ, Maxwell ES, Gupta R. Sequential 2'-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J Biol Chem 2004; 279:47661-71. [PMID: 15347671 DOI: 10.1074/jbc.m408868200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Haloferax volcanii pre-tRNA(Trp) processing requires box C/D ribonucleoprotein (RNP)-guided 2'-O-methylation of nucleotides C34 and U39 followed by intron excision. Positioning of the box C/D guide RNA within the intron of this pre-tRNA led to the assumption that nucleotide methylation is guided by the cis-positioned box C/D RNPs. We have now investigated the mechanism of 2'-O-methylation for the H. volcanii pre-tRNA(Trp) in vitro by assembling methylation-competent box C/D RNPs on both the pre-tRNA and the excised intron (both linear and circular forms) using Methanocaldococcus jannaschii box C/D RNP core proteins. With both kinetic studies and single nucleotide substitutions of target and guide nucleotides, we now demonstrate that pre-tRNA methylation is guided in trans by the intron-encoded box C/D RNPs positioned in either another pre-tRNA(Trp) or in the excised intron. Methylation by in vitro assembled RNPs prefers but does not absolutely require Watson-Crick pairing between the guide and target nucleotides. We also demonstrate for the first time that methylation of two nucleotides guided by a single box C/D RNA is sequential, that is, box C'/D' RNP-guided U39 methylation first requires box C/D RNP-guided methylation of C34. Methylation of the two nucleotides of exogenous pre-tRNA(Trp) added to an H. volcanii cell extract also occurs sequentially and is also accomplished in trans using RNPs that pre-exist in the extract. Thus, this trans mechanism is analogous to eukaryal pre-rRNA 2'-O-methylation guided by intron-encoded but trans-acting box C/D small nucleolar RNPs. This trans mechanism could explain the observed accumulation of the excised H. volcanii pre-tRNA(Trp) intron in vivo. A trans mechanism would also eliminate the obligatory refolding of the pre-tRNA that would be required to carry out two cis-methylation reactions before pre-tRNA splicing.
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MESH Headings
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Gene Expression Regulation, Archaeal
- Haloferax volcanii/genetics
- Haloferax volcanii/metabolism
- Introns
- Methylation
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Transfer, Trp/chemistry
- RNA, Transfer, Trp/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
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Affiliation(s)
- Sanjay K Singh
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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136
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Morlando M, Ballarino M, Greco P, Caffarelli E, Dichtl B, Bozzoni I. Coupling between snoRNP assembly and 3' processing controls box C/D snoRNA biosynthesis in yeast. EMBO J 2004; 23:2392-401. [PMID: 15167896 PMCID: PMC423293 DOI: 10.1038/sj.emboj.7600254] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Accepted: 05/04/2004] [Indexed: 11/08/2022] Open
Abstract
RNA polymerase II transcribes genes encoding proteins and a large number of small stable RNAs. While pre-mRNA 3'-end formation requires a machinery ensuring tight coupling between cleavage and polyadenylation, small RNAs utilize polyadenylation-independent pathways. In yeast, specific factors required for snRNA and snoRNA 3'-end formation were characterized as components of the APT complex that is associated with the core complex of the cleavage/polyadenylation machinery (core-CPF). Other essential factors were identified as independent components: Nrd1p, Nab3p and Sen1p. Here we report that mutations in the conserved box D of snoRNAs and in the snoRNP-specific factor Nop1p interfere with transcription and 3'-end formation of box C/D snoRNAs. We demonstrate that Nop1p is associated with box C/D snoRNA genes and that it interacts with APT components. These data suggest a mechanism of quality control in which efficient transcription and 3'-end formation occur only when nascent snoRNAs are successfully assembled into functional particles.
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Affiliation(s)
- Mariangela Morlando
- Department of Genetics and Molecular Biology, Institute Pasteur Cenci-Bolognetti, University of Rome ‘La Sapienza', Rome, Italy
| | - Monica Ballarino
- Department of Genetics and Molecular Biology, Institute Pasteur Cenci-Bolognetti, University of Rome ‘La Sapienza', Rome, Italy
| | - Paolo Greco
- Department of Genetics and Molecular Biology, Institute Pasteur Cenci-Bolognetti, University of Rome ‘La Sapienza', Rome, Italy
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology of CNR, University of Rome ‘La Sapienza', Rome, Italy
| | - Bernhard Dichtl
- Department of Cell Biology, Biozentrum, University of Basel, Klingelbergstrasse, Basel, Switzerland
| | - Irene Bozzoni
- Department of Genetics and Molecular Biology, Institute Pasteur Cenci-Bolognetti, University of Rome ‘La Sapienza', Rome, Italy
- Institute of Molecular Biology and Pathology of CNR, University of Rome ‘La Sapienza', Rome, Italy
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137
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Moore T, Zhang Y, Fenley MO, Li H. Molecular Basis of Box C/D RNA-Protein Interactions. Structure 2004; 12:807-18. [PMID: 15130473 DOI: 10.1016/j.str.2004.02.033] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2003] [Revised: 02/10/2004] [Accepted: 02/10/2004] [Indexed: 11/20/2022]
Abstract
We have determined and refined a crystal structure of the initial assembly complex of archaeal box C/D sRNPs comprising the Archaeoglobus fulgidus (AF) L7Ae protein and a box C/D RNA. The box C/D RNA forms a classical kink-turn (K-turn) structure and the resulting protein-RNA complex serves as a distinct platform for recruitment of the fibrillarin-Nop5p complex. The cocrystal structure confirms previously proposed secondary structure of the box C/D RNA that includes a protruded U, a UU mismatch, and two sheared tandem GA base pairs. Detailed structural comparisons of the AF L7Ae-box C/D RNA complex with previously determined crystal structures of L7Ae homologs in complex with functionally distinct K-turn RNAs revealed a set of remarkably conserved principles in protein-RNA interactions. These analyses provide a structural basis for interpreting the functional roles of the box C/D sequences in directing specific assembly of box C/D sRNPs.
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Affiliation(s)
- Terrie Moore
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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138
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Hamma T, Ferré-D'Amaré AR. Structure of Protein L7Ae Bound to a K-Turn Derived from an Archaeal Box H/ACA sRNA at 1.8 Å Resolution. Structure 2004; 12:893-903. [PMID: 15130481 DOI: 10.1016/j.str.2004.03.015] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Revised: 12/17/2003] [Accepted: 02/11/2004] [Indexed: 11/17/2022]
Abstract
The archaeal RNA binding protein L7Ae and its eukaryotic homolog 15.5 kDa/Snu13 recognize K-turns. This structural motif is canonically comprised of two stems (one with tandem A.G base pairs, the other with Watson-Crick pairs) linked by an asymmetric internal loop. L7Ae recognizes conventional K-turns in ribosomal and box C/D RNAs but also binds specifically to some box H/ACA RNAs at terminal stem loops. These have the A.G paired stem, but lack the Watson-Crick stem. The structure of Methanococcus jannaschii L7Ae bound to a symmetric duplex RNA without Watson-Crick stems demonstrates how a binding site for this component of diverse ribonucleoprotein complexes can be constructed with only the A.G stem and the loop. The RNA adopts a functional conformation with the aid of a base triple and tight binding of divalent cations. Comparison with the 15.5 kDa/Snu13-RNA complex structure suggests why the eukaryotic homolog does not recognize terminal stem loop L7Ae binding sites.
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Affiliation(s)
- Tomoko Hamma
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA
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139
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Bortolin ML, Bachellerie JP, Clouet-d'Orval B. In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp). Nucleic Acids Res 2004; 31:6524-35. [PMID: 14602911 PMCID: PMC275556 DOI: 10.1093/nar/gkg860] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Among the large family of C/D methylation guide RNAs, the intron of euryarchaeal pre-tRNA(Trp) represents an outstanding specimen able to guide in cis, instead of in trans, two 2'-O-methylations in the pre-tRNA exons. Remarkably, both sites of methylation involve nucleotides within the bulge-helix-bulge (BHB) splicing motif, while the RNA-guided methylation and pre-tRNA splicing events depend on mutually exclusive RNA folding patterns. Using the three recombinant core proteins of archaeal C/D RNPs, we have analyzed in vitro RNP assembly of the pre-tRNA and tested its site-specific methylation activity. Recognition by L7Ae of hallmark K-turns at the C/D and C'/D' motifs appears as a crucial assembly step required for subsequent binding of a Nop5p-aFib heterodimer at each site. Unexpectedly, however, even without L7Ae but at a higher concentration of Nop5p-aFib, a substantially active RNP complex can still form, possibly reflecting the higher propensity of the cis-acting system to form guide RNA duplex(es) relative to classical trans- acting C/D RNA guides. Moreover, footprinting data of RNPs, consistent with Nop5p interacting with the non-canonical stem of the K-turn, suggest that binding of Nop5p-aFib to the pre-tRNA-L7Ae complex might direct transition from a splicing-competent structure to an RNA conformer displaying the guide RNA duplexes required for site-specific methylation.
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Affiliation(s)
- Marie-Line Bortolin
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099 du CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
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140
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Deng L, Starostina NG, Liu ZJ, Rose JP, Terns RM, Terns MP, Wang BC. Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem Biophys Res Commun 2004; 315:726-32. [PMID: 14975761 DOI: 10.1016/j.bbrc.2004.01.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2004] [Indexed: 11/30/2022]
Abstract
The methyltransferase fibrillarin is the catalytic component of ribonucleoprotein complexes that direct site-specific methylation of precursor ribosomal RNA and are critical for ribosome biogenesis in eukaryotes and archaea. Here we report the crystal structure of a fibrillarin ortholog from the hyperthermophilic archaeon Pyrococcus furiosus at 1.97A resolution. Comparisons of the X-ray structures of fibrillarin orthologs from Methanococcus jannashii and Archaeoglobus fulgidus reveal nearly identical backbone configurations for the catalytic C-terminal domain with the exception of a unique loop conformation at the S-adenosyl-l-methionine (AdoMet) binding pocket in P. furiosus. In contrast, the N-terminal domains are divergent which may explain why some forms of fibrillarin apparently homodimerize (M. jannashii) while others are monomeric (P. furiosus and A. fulgidus). Three positively charged amino acids surround the AdoMet-binding site and sequence analysis indicates that this is a conserved feature of both eukaryotic and archaeal fibrillarins. We discuss the possibility that these basic residues of fibrillarin are important for RNA-guided rRNA methylation.
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Affiliation(s)
- Lu Deng
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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141
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Yanagida M, Hayano T, Yamauchi Y, Shinkawa T, Natsume T, Isobe T, Takahashi N. Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes. J Biol Chem 2003; 279:1607-14. [PMID: 14583623 DOI: 10.1074/jbc.m305604200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Fibrillarin (FIB, Nop1p in yeast) is an RNA methyltransferase found not only in the fibrillar region of the nucleolus but also in Cajal bodies. FIB is essential for efficient processing of preribosomal RNA during ribosome biogenesis, although its precise function in this process and its role in Cajal bodies remain uncertain. Here, we demonstrate that the human FIB N-terminal glycine- and arginine-rich domain (residues 1-77) and its spacer region 1 (78-132) interact with splicing factor 2-associated p32 (SF2A-p32) and that the FIB methyltransferase-like domain (133-321) interacts with protein-arginine methyltransferase 5 (PRMT5, Janus kinase-binding protein 1). We also show that these proteins associate with several additional proteins, including PRMT1, tubulin alpha 3, and tubulin beta 1 to form a sub-complex that is principally independent of the association of FIB with preribosomal ribonucleoprotein complexes that co-immunoprecipitate with the sub-complex in human cells expressing FLAG-tagged FIB. Based on the physical association of FIB with SF2A-p32 and PRMTs, as well as the other reported results, we propose that FIB may coordinate both RNA and protein methylation during the processes of ribosome biogenesis in the nucleolus and RNA editing such as small nuclear (nucleolar) ribonucleoprotein biogenesis in Cajal bodies.
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Affiliation(s)
- Mitsuaki Yanagida
- Department of Applied Biological Science, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509
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142
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Rashid R, Aittaleb M, Chen Q, Spiegel K, Demeler B, Li H. Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J Mol Biol 2003; 333:295-306. [PMID: 14529617 DOI: 10.1016/j.jmb.2003.08.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Box C/D small ribonucleoprotein particles (sRNPs) are archaeal homologs of small nucleolar ribonucleoprotein particles (snoRNPs) in eukaryotes that are responsible for site specific 2'-O-methylation of ribosomal and transfer RNAs. The function of box C/D sRNPs is characterized by step-wise assembly of three core proteins around a box C/D RNA that include fibrillarin, Nop5p, and L7Ae. The most distinct structural feature in all box C/D RNAs is the presence of two conserved box C/D motifs accompanied by often a single, and sometimes two, antisense elements located immediately upstream of either the D or D' box. Despite this asymmetric distribution of antisense elements, the bipartite feature of the box C/D motifs appears to be in pleasing agreement with a recently reported three-dimensional structure of the core protein complex between fibrillarin and Nop5p. This investigates functional implications of the symmetric features both in box C/D RNAs and in the fibrillarin-Nop5p complex. Site-directed mutagenesis was employed to generate box C/D RNAs lacking one of the two box C/D motifs and a mutant fibrillarin-Nop5p complex deficient in self-association. The ability of the mutated components to assemble and to direct methyl transfer reactions was assessed by gel mobility-shift, analytical ultracentrifugation, and in vitro catalysis studies. The results presented here suggest that, while a box C/D sRNP is capable of asymmetrical assembly, the symmetries in both the box C/D RNA and in the fibrillarin-Nop5p complex are required for efficient catalysis. These findings underscore the importance of functional assembly in methyl transfer reactions.
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MESH Headings
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Archaeoglobus fulgidus/genetics
- Archaeoglobus fulgidus/metabolism
- Base Pairing
- Base Sequence
- Binding Sites
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Dimerization
- Electrophoretic Mobility Shift Assay
- Methylation
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nuclear Proteins
- RNA Editing
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- RNA, Small Untranslated
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Affiliation(s)
- Rumana Rashid
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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143
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Hayano T, Yanagida M, Yamauchi Y, Shinkawa T, Isobe T, Takahashi N. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome. J Biol Chem 2003; 278:34309-19. [PMID: 12777385 DOI: 10.1074/jbc.m304304200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Nop56p is a component of the box C/D small nucleolar ribonucleoprotein complexes that direct 2'-O-methylation of pre-rRNA during its maturation. Genetic analyses in yeast have shown that Nop56p plays important roles in the early steps of pre-rRNA processing. However, its precise function remains elusive, especially in higher eukaryotes. Here we describe the proteomic characterization of human Nop56p (hNop56p)-associated pre-ribosomal ribonucleoprotein complexes. Mass spectrometric analysis of purified pre-ribosomal ribonucleoprotein complexes identified 61 ribosomal proteins, 16 trans-acting factors probably involved in ribosome biogenesis, and 29 proteins whose function in ribosome biogenesis is unknown. Identification of pre-rRNA species within hNop56p-associated pre-ribosomal ribonucleoprotein complexes, coupled with the known functions of yeast orthologs of the probable trans-acting factors identified in human, demonstrated that hNop56p functions in the early to middle stages of 60 S subunit synthesis in human cells. Interestingly, the nucleolar phosphoprotein treacle, which is responsible for the craniofacial disorder associated with Treacher Collins syndrome, was found to be a constituent of hNop56p-associated pre-rRNP complexes. The association of hNop56p and treacle within the complexes was independent of rRNA integrity, indicating a direct interaction. In addition, the protein compositions of the treacle-associated and hNop56p-associated pre-ribosomal ribonucleoprotein complexes were very similar, suggesting functional similarities between these two complexes with respect to ribosome biogenesis in human cells.
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Affiliation(s)
- Toshiya Hayano
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509
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144
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Tran EJ, Zhang X, Maxwell ES. Efficient RNA 2'-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs. EMBO J 2003; 22:3930-40. [PMID: 12881427 PMCID: PMC169041 DOI: 10.1093/emboj/cdg368] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Box C/D ribonucleoprotein (RNP) complexes direct the nucleotide-specific 2'-O-methylation of ribonucleotide sugars in target RNAs. In vitro assembly of an archaeal box C/D sRNP using recombinant core proteins L7, Nop56/58 and fibrillarin has yielded an RNA:protein enzyme that guides methylation from both the terminal box C/D core and internal C'/D' RNP complexes. Reconstitution of sRNP complexes containing only box C/D or C'/D' motifs has demonstrated that the terminal box C/D RNP is the minimal methylation-competent particle. However, efficient ribonucleotide 2'-O-methylation requires that both the box C/D and C'/D' RNPs function within the full-length sRNA molecule. In contrast to the eukaryotic snoRNP complex, where the core proteins are distributed asymmetrically on the box C/D and C'/D' motifs, all three archaeal core proteins bind both motifs symmetrically. This difference in core protein distribution is a result of altered RNA-binding capabilities of the archaeal and eukaryotic core protein homologs. Thus, evolution of the box C/D nucleotide modification complex has resulted in structurally distinct archaeal and eukaryotic RNP particles.
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Affiliation(s)
- Elizabeth J Tran
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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145
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Hirose T, Shu MD, Steitz JA. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell 2003; 12:113-23. [PMID: 12887897 DOI: 10.1016/s1097-2765(03)00267-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In mammalian cells, all small nucleolar RNAs (snoRNAs) that guide rRNA modification are encoded within the introns of host genes. An optimal position about 70 nts upstream of the 3' splice site of the host intron is critical for efficient expression of box C/D snoRNAs in vivo, suggesting synergy with splicing. Here, we have used a coupled in vitro splicing-snoRNA processing system to demonstrate that assembly of box C/D snoRNP proteins is the step affected by snoRNA location, and that active splicing is essential for snoRNP assembly. Splicing blockage experiments further reveal that snoRNP proteins bind specifically at the spliceosomal C1 complex stage. In contrast, splicing-independent snoRNP assembly can occur in vitro on snoRNAs that possess stable external stems. In vivo analyses confirm that a stable stem can compensate for the unusual position of those few box C/D snoRNAs located far from the 3' splice site of their host intron.
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Affiliation(s)
- Tetsuro Hirose
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
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146
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Abstract
It has been known for nearly half a century that coding and non-coding RNAs (mRNA, and tRNAs and rRNAs respectively) play critical roles in the process of information transfer from DNA to protein. What is both surprising and exciting, are the discoveries in the last decade that cells, particularly eukaryotic cells, contain a plethora of non-coding RNAs and that these RNAs can either possess catalytic activity or can function as integral components of dynamic ribonucleoprotein machines. These machines appear to mediate diverse, complex and essential processes such as intron excision, RNA modification and editing, protein targeting, DNA packaging, etc. Archaea have been shown to possess RNP complexes; some of these are authentic homologues of the eukaryotic complexes that function as machines in the processing, modification and assembly of rRNA into ribosomal subunits. Deciphering how these RNA-containing machines function will require a dissection and analysis of the component parts, an understanding of how the parts fit together and an ability to reassemble the parts into complexes that can function in vitro. This article summarizes our current knowledge about small-non-coding RNAs in Archaea, their roles in ribosome biogenesis and their relationships to the complexes that have been identified in eukaryotic cells.
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Affiliation(s)
- Arina D Omer
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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147
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Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H. Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Mol Biol 2003; 10:256-63. [PMID: 12598892 DOI: 10.1038/nsb905] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2002] [Accepted: 01/03/2003] [Indexed: 11/09/2022]
Abstract
Nop56p and Nop58p are two core proteins of the box C/D snoRNPs that interact concurrently with fibrillarin and snoRNAs to function in enzyme assembly and catalysis. Here we report the 2.9 A resolution co-crystal structure of an archaeal homolog of Nop56p/Nop58p, Nop5p, in complex with fibrillarin from Archaeoglobus fulgidus (AF) and the methyl donor S-adenosyl-L-methionine. The N-terminal domain of Nop5p forms a complementary surface to fibrillarin that serves to anchor the catalytic subunit and to stabilize cofactor binding. A coiled coil in Nop5p mediates dimerization of two fibrillarin-Nop5p heterodimers for optimal interactions with bipartite box C/D RNAs. Structural analysis and complementary biochemical data demonstrate that the conserved C-terminal domain of Nop5p harbors RNA-binding sites. A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Archaeoglobus fulgidus/genetics
- Archaeoglobus fulgidus/metabolism
- Binding Sites
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Crystallography, X-Ray
- Dimerization
- Electrophoretic Mobility Shift Assay
- Macromolecular Substances
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- Nuclear Proteins
- Protein Structure, Tertiary
- RNA Editing
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Sequence Homology, Amino Acid
- Static Electricity
- RNA, Small Untranslated
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Affiliation(s)
- Mohamed Aittaleb
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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148
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149
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Rozhdestvensky TS, Tang TH, Tchirkova IV, Brosius J, Bachellerie JP, Hüttenhofer A. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res 2003; 31:869-77. [PMID: 12560482 PMCID: PMC149196 DOI: 10.1093/nar/gkg175] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Small nucleolar RNAs (designated as snoRNAs in Eukarya or sRNAs in Archaea) can be grouped into H/ACA or C/D box snoRNA (sRNA) subclasses. In Eukarya, H/ACA snoRNAs assemble into a ribonucleoprotein (RNP) complex comprising four proteins: Cbf5p, Gar1p, Nop10p and Nhp2p. A homolog for the Nhp2p protein has not been identified within archaeal H/ACA RNPs thus far, while potential orthologs have been identified for the other three proteins. Nhp2p is related, particularly in the middle portion of the protein sequence, to the archaeal ribosomal protein and C/D box protein L7Ae. This finding suggests that L7Ae may be able to substitute for the Nhp2p protein in archaeal H/ACA sRNAs. By band shift assays, we have analyzed in vitro the interaction between H/ACA box sRNAs and protein L7Ae from the archaeon Archaeoglobus fulgidus. We present evidence that L7Ae forms specific complexes with three different H/ACA sRNAs, designated as Afu-4, Afu-46 and Afu-190 with an apparent K(d) ranging from 28 to 100 nM. By chemical and enzymatic probing we show that distinct bases located within bulges or loops of H/ACA sRNAs interact with the L7Ae protein. These findings are corroborated by mutational analysis of the L7Ae binding site. Thereby, the RNA motif required for L7Ae binding exhibits a structure, designated as the K-turn, which is present in all C/D box sRNAs. We also identified four H/ACA RNAs from the archaeal species Pyrococcus which exhibit the K-turn motif at a similar position in their structure. These findings suggest a triple role for L7Ae protein in Archaea, e.g. in ribosomes as well as H/ACA and C/D box sRNP biogenesis and function by binding to the K-turn motif.
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Affiliation(s)
- Timofey S Rozhdestvensky
- Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität Münster, D-48149 Münster, Germany
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150
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Affiliation(s)
- Wayne A Decatur
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA
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