1
|
Andrade-Salas A, Canela-Pérez I, Cevallos AM, López-Villaseñor I, Hernández R. Trypanosoma cruzi Fibrillarins: Two paralogous proteins with non-identical signals for nuclear transport. Biochem Biophys Res Commun 2023; 682:274-280. [PMID: 37832384 DOI: 10.1016/j.bbrc.2023.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023]
Abstract
Trypanosoma cruzi is a parasitic protozoa causative of Chagas disease. As part of our interest in studying the basic biology of this microorganism, this work reports our observations related to the characterization of motifs and structural domains present in two fibrillarin isoforms (TcFib1 and TcFib2) that were found to be necessary for the nuclear targeting of these nucleolar proteins. Previous characterization of these proteins indicated that they share 68.67% of identical amino acids and are both expressed as nucleolar proteins in T. cruzi epimastigotes. Using an approach based on the transfection of recombinant genes encoding fluorescent fibrillarin-EGFP fusion proteins, this study found evidence for the presence of 4 motifs or protein domains that help target these proteins to the nucleus: The GAR domain and carboxyl terminus in both TcFibs, as well as two lysines and a computationally predicted cNLS in TcFib1. As a distinctive feature, the GAR domain of TcFib2 proved to be essential for the nuclear localization of this protein paralog. Such a difference between TcFib1 and Tcfib2 nuclear localization signals can be explained as the presence of two partially related nuclear import pathways for the two fibrillarin homologues in this organism.
Collapse
Affiliation(s)
- Arturo Andrade-Salas
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Israel Canela-Pérez
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico.
| |
Collapse
|
2
|
Decle-Carrasco S, Rodríguez-Piña AL, Rodríguez-Zapata LC, Castano E. Current research on viral proteins that interact with fibrillarin. Mol Biol Rep 2023; 50:4631-4643. [PMID: 36928641 PMCID: PMC10018631 DOI: 10.1007/s11033-023-08343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
The nucleolus is a multifunctional nuclear domain primarily dedicated to ribosome biogenesis. Certain viruses developed strategies to manipulate host nucleolar proteins to facilitate their replication by modulating ribosomal RNA (rRNA) processing. This association interferes with nucleolar functions resulting in overactivation or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and affecting stress response. The nucleolar protein fibrillarin (FBL) is an important target of some plant and animal viruses. FBL is an essential and highly conserved S-adenosyl methionine (SAM) dependent methyltransferase, capable of rRNA degradation by its intrinsically disordered region (IDR), the glycine/arginine-rich (GAR) domain. It forms a ribonucleoprotein complex that directs 2'-O-methylations in more than 100 sites of pre-rRNAs. It is involved in multiple cellular processes, including initiation of transcription, oncogenesis, and apoptosis, among others. The interaction with animal viruses, including human viruses, triggered its redistribution to the nucleoplasm and cytoplasm, interfering with its role in pre-rRNA processing. Viral-encoded proteins with IDRs as nucleocapsids, matrix, Tat protein, and even a viral snoRNA, can associate with FBL, forcing the nucleolar protein to undergo atypical functions. Here we review the molecular mechanisms employed by animal and human viruses to usurp FBL functions and the effect on cellular processes, particularly in ribosome biogenesis.
Collapse
Affiliation(s)
- Stefano Decle-Carrasco
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Alma Laura Rodríguez-Piña
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Enrique Castano
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México.
| |
Collapse
|
3
|
Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H. Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res 2020; 47:10942-10955. [PMID: 31586407 PMCID: PMC6847430 DOI: 10.1093/nar/gkz856] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/20/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022] Open
Abstract
The complex between Trm7 and Trm734 (Trm7–Trm734) from Saccharomyces cerevisiae catalyzes 2′-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7–Trm734 complex. Purified recombinant Trm7–Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7–Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7–Trm734. Small angle X-ray scattering reveals that Trm7–Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7–Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
Collapse
Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Keisuke Okada
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kazuaki Yoshii
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Shiraishi
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shinya Saijo
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
- To whom correspondence should be addressed. Tel: +81 89 927 8548; Fax: +81 89 927 9941;
| |
Collapse
|
4
|
Probing the mechanisms underlying human diseases in making ribosomes. Biochem Soc Trans 2017; 44:1035-44. [PMID: 27528749 DOI: 10.1042/bst20160064] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 12/26/2022]
Abstract
Ribosomes are essential, highly complex machines responsible for protein synthesis in all growing cells. Because of their importance, the process of building these machines is intricately regulated. Although the proteins involved in regulating ribosome biogenesis are just beginning to be understood, especially in human cells, the consequences for dysregulating this process have been even less studied. Such interruptions in ribosome synthesis result in a collection of human disorders known as ribosomopathies. Ribosomopathies, which occur due to mutations in proteins involved in the global process of ribosome biogenesis, result in tissue-specific defects. The questions posed by this dichotomy and the steps taken to address these questions are therefore the focus of this review: How can tissue-specific disorders result from alterations in global processes? Could ribosome specialization account for this difference?
Collapse
|
5
|
Shubina MY, Musinova YR, Sheval EV. Nucleolar methyltransferase fibrillarin: Evolution of structure and functions. BIOCHEMISTRY (MOSCOW) 2016; 81:941-50. [DOI: 10.1134/s0006297916090030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
6
|
Rodriguez-Corona U, Sobol M, Rodriguez-Zapata LC, Hozak P, Castano E. Fibrillarin from Archaea to human. Biol Cell 2015; 107:159-74. [PMID: 25772805 DOI: 10.1111/boc.201400077] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022]
Abstract
Fibrillarin is an essential protein that is well known as a molecular marker of transcriptionally active RNA polymerase I. Fibrillarin methyltransferase activity is the primary known source of methylation for more than 100 methylated sites involved in the first steps of preribosomal processing and required for structural ribosome stability. High expression levels of fibrillarin have been observed in several types of cancer cells, particularly when p53 levels are reduced, because p53 is a direct negative regulator of fibrillarin transcription. Here, we show fibrillarin domain conservation, structure and interacting molecules in different cellular processes as well as with several viral proteins during virus infection.
Collapse
Affiliation(s)
- Ulises Rodriguez-Corona
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Luis Carlos Rodriguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Enrique Castano
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| |
Collapse
|
7
|
Babski J, Maier LK, Heyer R, Jaschinski K, Prasse D, Jäger D, Randau L, Schmitz RA, Marchfelder A, Soppa J. Small regulatory RNAs in Archaea. RNA Biol 2014; 11:484-93. [PMID: 24755959 PMCID: PMC4152357 DOI: 10.4161/rna.28452] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs and siRNAs typically bind to the 3′-untranslated region (3′-UTR) of their target mRNAs and influence translation efficiency and/or mRNA stability. In archaea, sRNAs have been identified in all species investigated using bioinformatic approaches, RNomics, and RNA-Seq. Their size can vary significantly between less than 50 to more than 500 nucleotides. Differential expression of sRNA genes has been studied using northern blot analysis, microarrays, and RNA-Seq. In addition, biological functions have been unraveled by genetic approaches, i.e., by characterization of designed mutants. As in bacteria, it was revealed that archaeal sRNAs are involved in many biological processes, including metabolic regulation, adaptation to extreme conditions, stress responses, and even in regulation of morphology and cellular behavior. Recently, the first target mRNAs were identified in archaea, including one sRNA that binds to the 5′-region of two mRNAs in Methanosarcina mazei Gö1 and a few sRNAs that bind to 3′-UTRs in Sulfolobus solfataricus, three Pyrobaculum species, and Haloferax volcanii, indicating that archaeal sRNAs appear to be able to target both the 5′-UTR or the 3′-UTRs of their respective target mRNAs. In addition, archaea contain tRNA-derived fragments (tRFs), and one tRF has been identified as a major ribosome-binding sRNA in H. volcanii, which downregulates translation in response to stress. Besides regulatory sRNAs, archaea contain further classes of sRNAs, e.g., CRISPR RNAs (crRNAs) and snoRNAs.
Collapse
Affiliation(s)
- Julia Babski
- Institute for Molecular Biosciences; Biocentre; Goethe University; Frankfurt, Germany
| | | | - Ruth Heyer
- Biology II; Ulm University; Ulm, Germany
| | - Katharina Jaschinski
- Institute for Molecular Biosciences; Biocentre; Goethe University; Frankfurt, Germany
| | - Daniela Prasse
- Institute for Microbiology; Christian-Albrechts-University; Kiel, Germany
| | - Dominik Jäger
- Institute for Microbiology; Christian-Albrechts-University; Kiel, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group; Max Planck Institute for Terrestrial Microbiology; Marburg, Germany
| | - Ruth A Schmitz
- Institute for Microbiology; Christian-Albrechts-University; Kiel, Germany
| | | | - Jörg Soppa
- Institute for Molecular Biosciences; Biocentre; Goethe University; Frankfurt, Germany
| |
Collapse
|
8
|
de Silva U, Zhou Z, Brown BA. Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:854-9. [PMID: 22869109 DOI: 10.1107/s1744309112026528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/12/2012] [Indexed: 11/10/2022]
Abstract
Fibrillarin is the key methyltransferase associated with the C/D class of small nuclear ribonucleoproteins (snRNPs) and participates in the preliminary step of pre-ribosomal rRNA processing. This molecule is found in the fibrillar regions of the eukaryotic nucleolus and is involved in methylation of the 2'-O atom of ribose in rRNA. Human fibrillarin contains an N-terminal GAR domain, a central RNA-binding domain comprising an RNP-2-like superfamily consensus sequence and a catalytic C-terminal helical domain. Here, Aeropyrum pernix fibrillarin is described, which is homologous to the C-terminal domain of human fibrillarin. The protein was crystallized with an S-adenosyl-L-methionine (SAM) ligand bound in the active site. The molecular structure of this complex was solved using X-ray crystallography at a resolution of 1.7 Å using molecular replacement with fibrillarin structural homologs. The structure shows the atomic details of SAM and its active-site interactions; there are a number of conserved residues that interact directly with the cofactor. Notably, the adenine ring of SAM is stabilized by π-π interactions with the conserved residue Phe110 and by electrostatic interactions with the Asp134, Ala135 and Gln157 residues. The π-π interaction appears to play a critical role in stabilizing the association of SAM with fibrillarin. Furthermore, comparison of A. pernix fibrillarin with homologous structures revealed different orientations of Phe110 and changes in α-helix 6 of fibrillarin and suggests key differences in its interactions with the adenine ring of SAM in the active site and with the C/D RNA. These differences may play a key role in orienting the SAM ligand for catalysis as well as in the assembly of other ribonucleoproteins and in the interactions with C/D RNA.
Collapse
Affiliation(s)
- Udesh de Silva
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | | | | |
Collapse
|
9
|
Tomkuviene M, Clouet-d'Orval B, Cerniauskas I, Weinhold E, Klimasauskas S. Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases. Nucleic Acids Res 2012; 40:6765-73. [PMID: 22564896 PMCID: PMC3413156 DOI: 10.1093/nar/gks381] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biophysical and mechanistic investigation of RNA function requires site-specific incorporation of spectroscopic and chemical probes, which is difficult to achieve using current technologies. We have in vitro reconstituted a functional box C/D small ribonucleoprotein RNA 2′-O-methyltransferase (C/D RNP) from the thermophilic archaeon Pyrococcus abyssi and demonstrated its ability to transfer a prop-2-ynyl group from a synthetic cofactor analog to a series of preselected target sites in model tRNA and pre-mRNA molecules. Target selection of the RNP was programmed by changing a dodecanucleotide guide sequence in a 64-nt C/D guide RNA leading to efficient derivatization of three out of four new targets in each RNA substrate. We also show that the transferred terminal alkyne can be further appended with a fluorophore using a bioorthogonal azide-alkyne 1,3-cycloaddition (click) reaction. The described approach for the first time permits synthetically tunable sequence-specific labeling of RNA with single-nucleotide precision.
Collapse
Affiliation(s)
- Migle Tomkuviene
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | | | | | | | | |
Collapse
|
10
|
Hardin JW, Reyes FE, Batey RT. Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex. J Biol Chem 2009; 284:15317-24. [PMID: 19336398 PMCID: PMC2685712 DOI: 10.1074/jbc.m901368200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 11/06/2022] Open
Abstract
In archaea and eukarya, box C/D ribonucleoprotein (RNP) complexes are responsible for 2'-O-methylation of tRNAs and rRNAs. The archaeal box C/D small RNP complex requires a small RNA component (sRNA) possessing Watson-Crick complementarity to the target RNA along with three proteins: L7Ae, Nop5p, and fibrillarin. Transfer of a methyl group from S-adenosylmethionine to the target RNA is performed by fibrillarin, which by itself has no affinity for the sRNA-target duplex. Instead, it is targeted to the site of methylation through association with Nop5p, which in turn binds to the L7Ae-sRNA complex. To understand how Nop5p serves as a bridge between the targeting and catalytic functions of the box C/D small RNP complex, we have employed alanine scanning to evaluate the interaction between the Pyrococcus horikoshii Nop5p domain and an L7Ae box C/D RNA complex. From these data, we were able to construct an isolated RNA-binding domain (Nop-RBD) that folds correctly as demonstrated by x-ray crystallography and binds to the L7Ae box C/D RNA complex with near wild type affinity. These data demonstrate that the Nop-RBD is an autonomously folding and functional module important for protein assembly in a number of complexes centered on the L7Ae-kinkturn RNP.
Collapse
Affiliation(s)
- John W Hardin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
| | | | | |
Collapse
|
11
|
Oruganti S, Zhang Y, Li H, Robinson H, Terns MP, Terns RM, Yang W, Li H. Alternative Conformations of the Archaeal Nop56/58-Fibrillarin Complex Imply Flexibility in Box C/D RNPs. J Mol Biol 2007; 371:1141-50. [PMID: 17617422 DOI: 10.1016/j.jmb.2007.06.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 06/05/2007] [Accepted: 06/12/2007] [Indexed: 12/31/2022]
Abstract
The Nop56/58-fibrillarin heterocomplex is a core protein complex of the box C/D ribonucleoprotein particles that modify and process ribosomal RNAs. The previous crystal structure of the Archaeoglobus fulgidus complex revealed a symmetric dimer of two Nop56/58-fibrillarin complexes linked by the coiled-coil domains of the Nop56/68 proteins. However, because the A. fulgidus Nop56/58 protein lacks some domains found in most other species, it was thought that the bipartite architecture of the heterocomplex was not likely a general phenomenon. Here we report the crystal structure of the Nop56/58-fibrillarin complex bound with methylation cofactor, S-adenosyl-L-methionine from Pyrococcus furiosus, at 2.7 A. The new complex confirms the generality of the previously observed bipartite arrangement. In addition however, the conformation of Nop56/58 in the new structure differs substantially from that in the earlier structure. The distinct conformations of Nop56/58 suggest potential flexibility in Nop56/58. Computational normal mode analysis supports this view. Importantly, fibrillarin is repositioned within the two complexes. We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA.
Collapse
Affiliation(s)
- Sri Oruganti
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | | | | | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
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
Collapse
Affiliation(s)
- A Gregory Matera
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106-4955, USA.
| | | | | |
Collapse
|
13
|
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: 273] [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.
Collapse
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
| |
Collapse
|
14
|
Kopp K, Gasiorowski JZ, Chen D, Gilmore R, Norton JT, Wang C, Leary DJ, Chan EKL, Dean DA, Huang S. Pol I transcription and pre-rRNA processing are coordinated in a transcription-dependent manner in mammalian cells. Mol Biol Cell 2006; 18:394-403. [PMID: 17108330 PMCID: PMC1783775 DOI: 10.1091/mbc.e06-03-0249] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pre-rRNA synthesis and processing are key steps in ribosome biogenesis. Although recent evidence in yeast suggests that these two processes are coupled, the nature of their association is unclear. In this report, we analyze the coordination between rDNA transcription and pre-rRNA processing in mammalian cells. We found that pol I transcription factor UBF interacts with pre-rRNA processing factors as analyzed by immunoprecipitations, and the association depends on active rRNA synthesis. In addition, injections of plasmids containing the human rDNA promoter and varying lengths of 18S rDNA into HeLa nuclei show that pol I transcription machinery can be recruited to rDNA promoters regardless of the product that is transcribed, whereas subgroups of pre-rRNA processing factors are recruited to plasmids only when specific pre-rRNA fragments are produced. Our observations suggest a model for sequential recruitment of pol I transcription factors and pre-rRNA processing factors to elongating pre-rRNA on an as-needed basis rather than corecruitment to sites of active transcription.
Collapse
Affiliation(s)
- K Kopp
- Department of Cell and Molecular Biology, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine Northwestern University, Chicago, IL 60611, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Makimoto Y, Yano H, Kaneta T, Sato Y, Sato S. Molecular cloning and gene expression of a fibrillarin homolog of tobacco BY-2 cells. PROTOPLASMA 2006; 229:53-62. [PMID: 17019528 DOI: 10.1007/s00709-006-0183-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Accepted: 11/02/2005] [Indexed: 05/12/2023]
Abstract
Fibrillarin is known to play an important role in precursor ribosomal RNA processing and ribosome assembly. The present study describes a fibrillarin homolog gene isolated from tobacco BY-2 cells and its expression during the cell cycle. The cDNA for a fibrillarin homolog, named NtFib1, was first cloned in Nicotiana tabacum with degenerate primers. It encodes 314 amino acids and the deduced amino acid sequence has some highly conserved functional domains, such as the glycine and arginine-rich (GAR) domain for nucleolar localization and the RNA-binding motif. The C-terminal region is highly conserved and has 7 beta-sheets and 7 alpha-helices which are peculiar to fibrillarin. Thus, it is suggested that the fibrillarin homolog of this plant species functions in the same way as the fibrillarin already known from human and yeast cells. Northern blot analysis of BY-2 cells synchronized with aphidicolin or a combination of aphidicolin and propyzamide showed that the histone H4 gene was specifically expressed in the S phase but NtFib1 mRNA remained at high levels during the cell cycle. Examination of the localization of NtFib1 protein tagged with green-fluorescent protein (GFP) suggested that some persisting in the mitotic apparatus was eventually incorporated into reconstructed nucleoli in late telophase. Newly synthesized GFP-tagged NtFib1 protein in the cytoplasm was added to the recycled protein in early mitosis. Highly concentrated actinomycin D completely inhibited the transcription of genes coding for rRNA (rDNA) but did not significantly suppress the amount of either NtFib1 mRNA or protein, although the NtFib1 protein was reversibly dislocated from nucleoli. Although hypoxic shock completely prohibited rDNA transcription, NtFib1 mRNA remained at the same level as in the control experiment, even after the 4 h treatment. These results indicate that the transcription of NtFib1 mRNA is not related to rDNA transcription and NtFib1 mRNA is resistant to disrupting factors during the cell cycle.
Collapse
MESH Headings
- Amino Acid Sequence
- Aphidicolin/pharmacology
- Benzamides/pharmacology
- Blotting, Northern
- Cell Cycle/genetics
- Cells, Cultured
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Dactinomycin/pharmacology
- Gene Expression Regulation, Plant/drug effects
- Gene Expression Regulation, Plant/genetics
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Microscopy, Fluorescence
- Molecular Sequence Data
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Nicotiana/cytology
- Nicotiana/drug effects
- Nicotiana/genetics
Collapse
Affiliation(s)
- Y Makimoto
- Department of Biology, Faculty of Science, Ehime University, Matsuyama, Japan
| | | | | | | | | |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
| | - Robert T. Batey
- To whom correspondence should be addressed. Tel: +1 303 735 2159; Fax: +1 303 735 1347;
| |
Collapse
|
17
|
Sato S, Yano H, Makimoto Y, Kaneta T, Sato Y. Nucleolonema as a fundamental substructure of the nucleolus. JOURNAL OF PLANT RESEARCH 2005; 118:71-81. [PMID: 15843864 DOI: 10.1007/s10265-005-0204-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 03/04/2005] [Indexed: 05/03/2023]
Abstract
The nucleolus is the most obvious structure in the eukaryotic nucleus. It is known to be a ribosome-producing apparatus where ribosomal (r) DNA is transcribed and the primary rRNA transcripts are processed to produce three of the four rRNA species. Electron microscopy has shown that the nucleolus consists of three major components, a dense fibrillar component (DFC), a granular component (GC) and a fibrillar center (FC). The DFC and FCs are integrated into a fundamental nucleolar substructure called the nucleolonema. The DFC corresponds to the matrix of the nucleolonema, and the FC is an electron microscopic counterpart of argyrophobic lacunae localized in the nucleolonema. The spherical FCs are intermittently arranged along the length of the nucleolonema in actively growing cells but are fused with each other to form tubular FCs when rDNA transcription is hampered. The RNase-gold complex does not bind to the FC but to the DFC and the GC, suggesting that rDNA transcription does not occur in the FC although both fluorescence in situ hybridization (FISH) and electron microscopic in situ hybridization reveal that the rDNA is specifically localized in the FCs. Immunogold-labeling after bromo-UTP (BrUTP) incorporation shows that rDNA transcription takes place in the boundary region between the FC and the DFC, and primary rRNA transcripts are expected to be processed outward within the DFC. Data have accumulated suggesting that the nucleolonema is a fundamental substructure of the nucleolus, and its skeleton is the tandem arrangement of the FCs, which are resting harbors or storages of rDNA. This paper proposes that the transversal structural organization of the nucleolonema is centrifugally built up by several structural and functional domains: condensed and/or loosened rDNA, rDNA transcription zone, and transcript processing and ribosome assembly zones.
Collapse
Affiliation(s)
- Seiichi Sato
- Department of Biology, Faculty of Science, Ehime University, Matsuyama, 790-8577, Japan.
| | | | | | | | | |
Collapse
|
18
|
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]
|
19
|
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.
Collapse
Affiliation(s)
- Mohamed Aittaleb
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | | | | | | |
Collapse
|