1
|
Mustoe AM, Al-Hashimi HM, Brooks CL. Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B 2014; 118:2615-27. [PMID: 24547945 PMCID: PMC3983386 DOI: 10.1021/jp411478x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Recent studies have shown that simple
stereochemical constraints
encoded at the RNA secondary structure level significantly restrict
the orientation of RNA helices across two-way junctions and yield
physically reasonable distributions of RNA 3D conformations. Here
we develop a new coarse-grain model, TOPRNA, that is optimized for
exploring detailed aspects of these topological constraints in complex
RNA systems. Unlike prior models, TOPRNA effectively treats RNAs as
collections of semirigid helices linked by freely rotatable single
strands, allowing us to isolate the effects of secondary structure
connectivity and sterics on 3D structure. Simulations of bulge junctions
show that TOPRNA captures new aspects of topological constraints,
including variations arising from deviations in local A-form structure,
translational displacements of the helices, and stereochemical constraints
imposed by bulge-linker nucleotides. Notably, these aspects of topological
constraints define free energy landscapes that coincide with the distribution
of bulge conformations in the PDB. Our simulations also quantitatively
reproduce NMR RDC measurements made on HIV-1 TAR at low salt concentrations,
although not for different TAR mutants or at high salt concentrations.
Our results confirm that topological constraints are an important
determinant of bulge conformation and dynamics and demonstrate the
utility of TOPRNA for studying the topological constraints of complex
RNAs.
Collapse
Affiliation(s)
- Anthony M Mustoe
- Departments of Biophysics and ‡Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | | | | |
Collapse
|
2
|
Ciganda M, Williams N. Characterization of a novel association between two trypanosome-specific proteins and 5S rRNA. PLoS One 2012; 7:e30029. [PMID: 22253864 PMCID: PMC3257258 DOI: 10.1371/journal.pone.0030029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/12/2011] [Indexed: 11/20/2022] Open
Abstract
P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are essential and are involved in ribosome biogenesis. Here, we show that these proteins interact in vitro with the 5S rRNA with nearly identical binding characteristics in the absence of other cellular factors. The T. brucei 5S rRNA has a complex secondary structure and presents four accessible loops (A to D) for interactions with RNA-binding proteins. In other eukaryotes, loop C is bound by the L5 ribosomal protein and loop A mainly by TFIIIA. The binding of P34 and P37 to T. brucei 5S rRNA involves the LoopA region of the RNA, but these proteins also protect the L5 binding site located on LoopC.
Collapse
Affiliation(s)
- Martin Ciganda
- Department of Microbiology and Immunology & Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, Buffalo, New York, United States of America
| | - Noreen Williams
- Department of Microbiology and Immunology & Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
| |
Collapse
|
3
|
Ciganda M, Williams N. Eukaryotic 5S rRNA biogenesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:523-33. [PMID: 21957041 DOI: 10.1002/wrna.74] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ribosome is a large complex containing both protein and RNA which must be assembled in a precise manner to allow proper functioning in the critical role of protein synthesis. 5S rRNA is the smallest of the RNA components of the ribosome, and although it has been studied for decades, we still do not have a clear understanding of its function within the complex ribosome machine. It is the only RNA species that binds ribosomal proteins prior to its assembly into the ribosome. Its transport into the nucleolus requires this interaction. Here we present an overview of some of the key findings concerning the structure and function of 5S rRNA and how its association with specific proteins impacts its localization and function.
Collapse
Affiliation(s)
- Martin Ciganda
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | | |
Collapse
|
4
|
Smirnov AV, Entelis NS, Krasheninnikov IA, Martin R, Tarassov IA. Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions. BIOCHEMISTRY (MOSCOW) 2009; 73:1418-37. [PMID: 19216709 DOI: 10.1134/s000629790813004x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Small non-coding RNAs are today a topic of great interest for molecular biologists because they can be regarded as relicts of a hypothetical "RNA world" which, apparently, preceded the modern stage of organic evolution on Earth. The small molecule of 5S rRNA (approximately 120 nucleotides) is a component of large ribosomal subunits of all living beings (5S rRNAs are not found only in mitoribosomes of fungi and metazoans). This molecule interacts with various protein factors and 23S (28S) rRNA. This review contains the accumulated data to date concerning 5S rRNA structure, interactions with other biological macromolecules, intracellular traffic, and functions in the cell.
Collapse
Affiliation(s)
- A V Smirnov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | | | | | | |
Collapse
|
5
|
Ma D, Lin Y, Xiao Z, Kappen L, Goldberg IH, Kallmerten AE, Jones GB. Designed DNA probes from the neocarzinostatin family: impact of glycosyl linkage stereochemistry on bulge base binding. Bioorg Med Chem 2009; 17:2428-32. [PMID: 19243952 DOI: 10.1016/j.bmc.2009.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 02/02/2009] [Accepted: 02/03/2009] [Indexed: 10/21/2022]
Abstract
Bulged sites in DNA and RNA have become targets for rational drug design due to their suspected involvement in a number of key biomolecular processes. A lead compound, derived from the enediyne natural product NCS-chrom has been used to inform chemical synthesis of a family of designed probes of DNA bulges, one of which shows 80 nM affinity for a two base bulged target. Key contributors to binding of these spirocyclic compounds have been studied in order to correlate affinity and specificity with structural features. Herein, we demonstrate that the glycosyl linkage stereochemistry of the pendant aminofucosyl group plays a pivotal role in binding, and coupled with insight obtained with various bulged targets, will allow rational design of second generation ligands.
Collapse
Affiliation(s)
- Dong Ma
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, 101HT, Boston, MA 02115, USA
| | | | | | | | | | | | | |
Collapse
|
6
|
Jeong HS, Kang S, Lee JY, Kim BH. Probing specific RNA bulge conformations by modified fluorescent nucleosides. Org Biomol Chem 2009; 7:921-5. [DOI: 10.1039/b816768k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
7
|
Smirnov A, Tarassov I, Mager-Heckel AM, Letzelter M, Martin RP, Krasheninnikov IA, Entelis N. Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria. RNA (NEW YORK, N.Y.) 2008; 14:749-59. [PMID: 18314502 PMCID: PMC2271358 DOI: 10.1261/rna.952208] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
RNA import into mitochondria is a widespread phenomenon. Studied in details for yeast, protists, and plants, it still awaits thorough investigation for human cells, in which the nuclear DNA-encoded 5S rRNA is imported. Only the general requirements for this pathway have been described, whereas specific protein factors needed for 5S rRNA delivery into mitochondria and its structural determinants of import remain unknown. In this study, a systematic analysis of the possible role of human 5S rRNA structural elements in import was performed. Our experiments in vitro and in vivo show that two distinct regions of the human 5S rRNA molecule are needed for its mitochondrial targeting. One of them is located in the proximal part of the helix I and contains a conserved uncompensated G:U pair. The second and most important one is associated with the loop E-helix IV region with several noncanonical structural features. Destruction or even destabilization of these sites leads to a significant decrease of the 5S rRNA import efficiency. On the contrary, the beta-domain of the 5S rRNA was proven to be dispensable for import, and thus it can be deleted or substituted without affecting the 5S rRNA importability. This finding was used to demonstrate that the 5S rRNA can function as a vector for delivering heterologous RNA sequences into human mitochondria. 5S rRNA-based vectors containing a substitution of a part of the beta-domain by a foreign RNA sequence were shown to be much more efficiently imported in vivo than the wild-type 5S rRNA.
Collapse
Affiliation(s)
- Alexandre Smirnov
- Department of Molecular and Cellular Genetics, UMR 7156, Centre National de Recherche Scientifique-Université Louis Pasteur,Strasbourg 67084, France
| | | | | | | | | | | | | |
Collapse
|
8
|
Jones GB, Lin Y, Xiao Z, Kappen L, Goldberg IH. Molecular probes of DNA bulges: Functional assay and spectroscopic analysis. Bioorg Med Chem 2007; 15:784-90. [PMID: 17085052 DOI: 10.1016/j.bmc.2006.10.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 10/22/2006] [Accepted: 10/23/2006] [Indexed: 11/30/2022]
Abstract
Bulged structures in DNA and RNA have been linked to biomolecular processes involved in numerous diseases, thus probes with affinity for these nucleic acid targets would be of considerable utility to chemical biologists. Herein, we report guided chemical synthesis of small molecules capable of binding to DNA bulges by virtue of their unique (spirocyclic) geometry. The agents, modeled on a natural product congener, show pronounced selectivity for specific bulged motifs and are able to enhance slipped DNA synthesis, a hallmark functional assay of bulge binding. Significantly, bulge-agent complexes demonstrate characteristic fluorescent signatures depending on bulge and flanking sequence in the oligo. It is anticipated that these signature patterns can be harnessed as molecular probes of bulged hotspots in DNA and RNA.
Collapse
Affiliation(s)
- Graham B Jones
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | | | | | | | | |
Collapse
|
9
|
Xiao Z, Zhang N, Lin Y, Jones GB, Goldberg IH. Spirocyclic helical compounds as binding agents for bulged RNA, including HIV-2 TAR. Chem Commun (Camb) 2006:4431-3. [PMID: 17057867 DOI: 10.1039/b610007d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on fluorescence binding studies and 1D 1H NMR studies, designed synthetic analogues of NCSi-gb bind specifically with two-base bulged RNA, including HIV-2 TAR RNA, making them potential lead compounds for antiviral drug development.
Collapse
Affiliation(s)
- Ziwei Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | |
Collapse
|
10
|
Kiparisov S, Petrov A, Meskauskas A, Sergiev PV, Dontsova OA, Dinman JD. Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae. Mol Genet Genomics 2005; 274:235-47. [PMID: 16047201 PMCID: PMC1276653 DOI: 10.1007/s00438-005-0020-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Accepted: 05/27/2005] [Indexed: 11/26/2022]
Abstract
5S rRNA extends from the central protuberance of the large ribosomal subunit, through the A-site finger, and down to the GTPase-associated center. Here, we present a structure-function analysis of seven 5S rRNA alleles which are sufficient for viability in the yeast Saccharomyces cerevisiae when expressed in the absence of wild-type 5S rRNAs, and extend this analysis using a large bank of mutant alleles that show semi-dominant phenotypes in the presence of wild-type 5S rRNA. This analysis supports the hypothesis that 5S rRNA serves to link together several different functional centers of the ribosome. Data are also presented which suggest that in eukaryotic genomes selection has favored the maintenance of multiple alleles of 5S rRNA, and that these may provide cells with a mechanism to post-transcriptionally regulate gene expression.
Collapse
|
11
|
Abstract
A library of random mutations in Xenopus ribosomal protein L5 was generated by error-prone PCR and used to delineate the binding domain for 5S rRNA. All but one of the amino acid substitutions that affected binding affinity are clustered in the central region of the protein. Several of the mutations are conservative substitutions of non-polar amino acid residues that are unlikely to form energetically significant contacts to the RNA. Thermal denaturation, monitored by circular dichroism (CD), indicates that L5 is not fully structured and association with 5S rRNA increases the t(m) of the protein by 16 degrees C. L5 induces changes in the CD spectrum of 5S rRNA, establishing that the complex forms by a mutual induced fit mechanism. Deuterium exchange reveals that a considerable amount of L5 is unstructured in the absence of 5S rRNA. The fluorescence emission of W266 provides evidence for structural changes in the C-terminal region of L5 upon binding to 5S rRNA; whereas, protection experiments demonstrate that the N terminus remains highly sensitive to protease digestion in the complex. Analysis of the amino acid sequence of L5 by the program PONDR predicts that the N and C-terminal regions of L5 are intrinsically disordered, but that the central region, which contains three essential tyrosine residues and other residues important for binding to 5S rRNA, is likely to be structured. Initial interaction of the protein with 5S rRNA likely occurs through this region, followed by induced folding of the C-terminal region. The persistent disorder in the N-terminal domain is possibly exploited for interactions between the L5-5S rRNA complex and other proteins.
Collapse
Affiliation(s)
- Jonathan P DiNitto
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | | |
Collapse
|
12
|
Szymański M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5 S rRNA: structure and interactions. Biochem J 2003; 371:641-51. [PMID: 12564956 PMCID: PMC1223345 DOI: 10.1042/bj20020872] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2002] [Revised: 01/28/2003] [Accepted: 02/04/2003] [Indexed: 11/17/2022]
Abstract
5 S rRNA is an integral component of the large ribosomal subunit in all known organisms. Despite many years of intensive study, the function of 5 S rRNA in the ribosome remains unknown. Advances in the analysis of ribosome structure that have revealed the crystal structures of large ribosomal subunits and of the complete ribosome from various organisms put the results of studies on 5 S rRNA in a new perspective. This paper summarizes recently published data on the structure and function of 5 S rRNA and its interactions in complexes with proteins, within and outside the ribosome.
Collapse
Affiliation(s)
- Maciej Szymański
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
| | | | | | | |
Collapse
|
13
|
Gerdeman MS, Henkin TM, Hines JV. Solution structure of the Bacillus subtilis T-box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility. J Mol Biol 2003; 326:189-201. [PMID: 12547201 DOI: 10.1016/s0022-2836(02)01339-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The T-box transcription antitermination regulatory system is an important mechanism for regulation of expression of aminoacyl-tRNA synthetase, amino acid biosynthesis and transporter gene expression in Gram-positive bacteria. Antitermination is dependent on a complex set of interactions between uncharged tRNA and the leader region of the mRNA of the regulated gene. Here, we report the solution structure of a model RNA, based on the Bacillus subtilis tyrS antiterminator, determined to an rmsd of 3.47A for all nine converged structures and 2.66A for the seven structures representing the consensus family. The antiterminator is comprised of two short helices with an intervening 7nt bulge. The bulge region of the antiterminator, which ultimately interacts with the acceptor end of tRNA, exhibits extensive stacking at the 3' end (encompassing the highly conserved ACC residues) and is the site of a pronounced kink between the two flanking helices. The 5' end of the bulge exhibits evidence of conformational flexibility. On the basis of the structural studies, there is no indication that the bases at the 5' end of the bulge that ultimately base-pair with tRNA are pre-organized for binding. Instead, the data are consistent with a model in which the stacking-induced structure at the 3' end of the bulge may facilitate the pre-selection of a set of conformations for the tRNA to sample during binding.
Collapse
MESH Headings
- Bacillus subtilis/genetics
- Base Pairing
- Base Sequence
- Conserved Sequence
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation
- Nucleotides/chemistry
- Nucleotides/genetics
- Pliability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Solutions
- Terminator Regions, Genetic/genetics
Collapse
Affiliation(s)
- Melinda S Gerdeman
- Division of Medicinal Chemistry, College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | | | | |
Collapse
|
14
|
DiNitto JP, Huber PW. A role for aromatic amino acids in the binding of Xenopus ribosomal protein L5 to 5S rRNA. Biochemistry 2001; 40:12645-53. [PMID: 11601989 DOI: 10.1021/bi011439m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of the Xenopus L5-5S rRNA complex depends on nonelectrostatic interactions. Fluorescence assays with 1-anilino-8-naphthalenesulfonate demonstrate that a hydrophobic region on L5 becomes exposed upon removal of bound 5S rRNA by treatment with ribonucleases. Several conserved aromatic amino acids, mostly tyrosines, were identified by comparative sequence analysis and changed individually to alanine. Substitution with alanine at any of three positions, Y86, Y99, or Y226, essentially abolishes RNA-binding activity, whereas those made at Y95 and Y207 have more modest effects. Replacement with phenylalanine at Y86 and Y226 does not change binding affinity, indicating that the aromatic ring of the side chain, not the hydroxyl group, is the critical functionality for binding. Alternatively, the phenolic hydroxyls at Y99 and Y207 do contribute to binding. The structural integrity of the mutant proteins was assessed using thermal denaturation and limited digestion with proteases. The T(m) of Y99A is 10 degrees C lower than that of the wild-type protein, and there are some differences in the protease digestion patterns that together indicate the structure of this mutant has been significantly perturbed. The structures of the other variants are not detectably different from the wild-type protein. These results provide evidence that intermolecular stacking interactions involving at least two tyrosine residues, Y86 and Y226, are necessary for formation of the L5-5S rRNA complex and can account, at least in part, for the contribution nonelectrostatic interactions make to the free energy of binding.
Collapse
Affiliation(s)
- J P DiNitto
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | |
Collapse
|