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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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2
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Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis. Proc Natl Acad Sci U S A 2022; 119:e2119529119. [PMID: 35238631 PMCID: PMC8915964 DOI: 10.1073/pnas.2119529119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Understanding and treating neurological disorders are global priorities. Some of these diseases are engendered by mutations that cause defects in the cellular synthesis of transfer RNAs (tRNAs), which function as adapter molecules that translate messenger RNAs into proteins. During tRNA biogenesis, ribonuclease P catalyzes removal of the transcribed sequence upstream of the mature tRNA. Here, we focus on a cytoplasmic tRNAArgUCU that is expressed specifically in neurons and, when harboring a particular point mutation, contributes to neurodegeneration in mice. Our results suggest that this mutation favors stable alternative structures that are not cleaved by mouse ribonuclease P and motivate a paradigm that may help to understand the molecular basis for disease-associated mutations in other tRNAs. n-Tr20 is a neuron-specific, cytoplasmic transfer RNAArgUCU (tRNAArgUCU) isodecoder that affects seizure susceptibility, neuronal excitability, and translation signaling in mice. In addition, the C50U substitution in n-Tr20 (n-Tr20C50U), which is found in the widely used C57BL/6J (B6J) inbred mouse line, contributes to neurodegeneration by epistatic interactions with mutations in Gtpbp1 or Gtpbp2, two factors that rescue ribosomal stalling. The brains of B6J mice have high levels of immature and low levels of mature n-Tr20C50U, implicating defective tRNA biogenesis as the basis for neuronal dysfunction, a hypothesis tested in this study. We demonstrate that partially purified mouse brain ribonuclease P, the endonuclease responsible for 5′ maturation of tRNAs, exhibits at 1 mM magnesium a 20-fold lower apparent cleavage rate for processing the n-Tr20C50U precursor than the wild-type precursor. Thermal denaturation studies unexpectedly revealed that substituting the native C50-G64 base pair with the U50-G64 wobble pair in n-Tr20C50U increased the Tm by as much as 8 °C, with the magnitude of the change dependent on [Mg2+]. Moreover, results from thermal denaturation, native gel electrophoresis, 1H nuclear magnetic resonance spectroscopy, and kinetic studies collectively support the presence of stable alternative folds for n-Tr20C50U that may also be sampled transiently and in low abundance by the wild-type tRNA. These findings suggest that mutation-driven restructuring could foster nonnative folds and that conformational toggling of tRNAs poses an intrinsic risk for dysfunction when point mutations selectively stabilize nonnative states. This model may be applicable for understanding the molecular basis of other diseases that are associated with tRNA mutations.
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3
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Fingerhut BP. The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface. Chem Commun (Camb) 2021; 57:12880-12897. [PMID: 34816825 PMCID: PMC8640580 DOI: 10.1039/d1cc05367a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022]
Abstract
The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions. Given the inherent complexity, suited model systems, carefully calibrated and benchmarked by experiments, are required to quantify the relevant interactions of RNA with the aqueous environment. In this feature article we summarize our recent progress in the understanding of the electrostatics at the biological interface of double stranded RNA (dsRNA) and transfer RNA (tRNA). Dimethyl phosphate (DMP) is introduced as a viable and rigorously accessible model system allowing the interaction strength with water molecules and counterions, their relevant fluctuation timescales and the spatial reach of interactions to be established. We find strong (up to ≈90 MV cm-1) interfacial electric fields with fluctuations extending up to ≈20 THz and demonstrate how the asymmetric stretching vibration νAS(PO2)- of the polarizable phosphate group can serve as the most sensitive probe for interfacial interactions, establishing a rigorous link between simulations and experiment. The approach allows for the direct interfacial observation of interactions of biologically relevant Mg2+ counterions with phosphate groups in contact pair geometries via the rise of a new absorption band imposed by exchange repulsion interactions at short interatomic distances. The systematic extension to RNA provides microscopic insights into the changes of the hydration structure that accompany the temperature induced melting of the dsRNA double helix and quantify the ionic interactions in the folded tRNA. The results show that pairs of negatively charged phosphate groups and Mg2+ ions represent a key structural feature of RNA embedded in water. They highlight the importance of binding motifs made of contact pairs in the electrostatic stabilization of RNA structures that have a strong impact on the surface potential and enable the fine tuning of the local electrostatic properties which are expected to be relevant for mediating the interactions between biomolecules.
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4
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Watanabe N, Suga K, Umakoshi H. Comparison of Physicochemical Membrane Properties of Vesicles Modified with Guanidinium Derivatives. J Phys Chem B 2017; 121:9213-9222. [PMID: 28820256 DOI: 10.1021/acs.jpcb.7b04007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bilayer vesicles have garnered considerable research attention as molecular vehicles capable of noncovalent interaction with biomolecules via electrostatic and hydrophobic bonds and van der Waals interactions. Guanidinium strongly interacts with phosphate groups. Thus, guanidinium modification of vesicles helps intensify the interaction between lipid membranes and nucleic acids. Here, two kinds of guanidinium derivatives, stearylguanidinium (SG) and myristoylarginine (MA), were synthesized and incorporated into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) vesicles. Differences in their membrane properties were evaluated using Fourier transform infrared spectroscopy, Raman spectroscopy, and the fluorescent probes 1,6-diphenyl-1,3,5-hexatriene (DPH), 6-lauroyl-2-dimethylaminonaphthalene (Laurdan), and 2-p-toluidinylnaphthalene-6-sulfonate (TNS). The increased SG ratio increased overall hydrophobicity and lipid packing density compared to POPC vesicles, and SG-modified vesicles successfully attracted and then denatured negatively charged tRNAs (tRNAs). In contrast, MA-modified vesicles did not affect the stiffness of POPC membranes, wherein no conformational change in tRNAs was observed in the presence of POPC/MA vesicles. Analyses of the pH-dependent fluorescence emission of TNS suggested that SG and MA molecules render the membrane surfaces cationic and anionic, respectively, which was also revealed by zeta potential measurements. Our results enabled the construction of a model of the headgroup orientation of zwitterionic POPC molecules controlled by modification with guanidinium derivatives. The results also indicate the possibility to regulate the interaction and conformation of biological molecules, such as nucleic acid.
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Affiliation(s)
- Nozomi Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University , 1-3 Machikaneyamacho, Toyonaka, Osaka 560-8531, Japan
| | - Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University , 1-3 Machikaneyamacho, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University , 1-3 Machikaneyamacho, Toyonaka, Osaka 560-8531, Japan
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5
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Power B, Rowe S, Fridgen TD. Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH3)]+ by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd). J Phys Chem B 2016; 121:58-65. [DOI: 10.1021/acs.jpcb.6b09614] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barry Power
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
| | - Steven Rowe
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
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6
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Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun 2016; 7:ncomms11768. [PMID: 27292179 PMCID: PMC4909931 DOI: 10.1038/ncomms11768] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/26/2016] [Indexed: 12/28/2022] Open
Abstract
Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining (15)N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k-1≈423 s(-1)) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the 'Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg(2+) or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways.
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Affiliation(s)
- Yi Xue
- Department of Biochemistry, Duke Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Brant Gracia
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, California 94305, USA.,Department of Chemistry, Stanford University, Stanford, California 94305, USA.,Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA.,Chemistry, Engineering, and Medicine for Human Health (ChEM-H) Institute, Stanford University, Stanford, California 94305, USA
| | - Rick Russell
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Chemistry, Duke University, Durham, Stanford, North Carolina 27710, USA
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7
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Power B, Haldys V, Salpin JY, Fridgen TD. Structures of [M(Ura-H)(H2 O)n ](+) (M = Mg, Ca, Sr, Ba; n = 1-3) complexes in the gas phase by IRMPD spectroscopy and theoretical studies. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:236-244. [PMID: 26956390 DOI: 10.1016/j.ijms.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/17/2023]
Abstract
The structures of singly and doubly (and for Mg, triply) hydrated group 2 metal dications bound to deprotonated uracil were explored in the gas phase using infrared multiple photon dissociation spectroscopy in the mid-infrared region (1000-1900 cm(-1) ) and the O-H/N-H stretching region (2700-3800 cm(-1) ) in a Fourier transform ion cyclotron resonance mass spectrometer. The infrared multiple photon dissociation spectra were then compared with the computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31 + G(d,p) basis set for all atoms except Ba(2+) and Sr(2+) , for which the LANL2DZ or the def2-TZVPP basis sets with relativistic core potentials were used. Atoms-in-molecules analysis was conducted for all lowest energy structures. The lowest energy isomers in all cases are those in which the one uracil is deprotonated at the N3 position, and the metal is coordinated to the N3 and O4 of uracil. Regardless of the degree of solvation, all water molecules are bound to the metal ion and participate in a hydrogen bond with a carbonyl of the uracil moiety.
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Affiliation(s)
- Barry Power
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
| | - Violette Haldys
- Université d'Evry Val d'Essonne - Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Bâtiment Maupertuis, Boulevard François Mitterrand, 91025, Evry, France
- CNRS UMR 8587
| | - Jean-Yves Salpin
- Université d'Evry Val d'Essonne - Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Bâtiment Maupertuis, Boulevard François Mitterrand, 91025, Evry, France
- CNRS UMR 8587
| | - Travis D Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
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8
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Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS). Arch Virol 2013; 159:235-48. [PMID: 23942952 PMCID: PMC3906528 DOI: 10.1007/s00705-013-1802-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/19/2013] [Indexed: 11/05/2022]
Abstract
Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted “modified panhandle” structure, the 5’ and 3’ termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3’- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3’ adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5’- and 3’-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties.
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9
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Nallagatla SR, Jones CN, Ghosh SKB, Sharma SD, Cameron CE, Spremulli LL, Bevilacqua PC. Native tertiary structure and nucleoside modifications suppress tRNA's intrinsic ability to activate the innate immune sensor PKR. PLoS One 2013; 8:e57905. [PMID: 23483938 PMCID: PMC3587421 DOI: 10.1371/journal.pone.0057905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/28/2013] [Indexed: 11/17/2022] Open
Abstract
Interferon inducible protein kinase PKR is an essential component of innate immunity. It is activated by long stretches of dsRNA and provides the first line of host defense against pathogens by inhibiting translation initiation in the infected cell. Many cellular and viral transcripts contain nucleoside modifications and/or tertiary structure that could affect PKR activation. We have previously demonstrated that a 5'-end triphosphate-a signature of certain viral and bacterial transcripts-confers the ability of relatively unstructured model RNA transcripts to activate PKR to inhibit translation, and that this activation is abrogated by certain modifications present in cellular RNAs. In order to understand the biological implications of native RNA tertiary structure and nucleoside modifications on PKR activation, we study here the heavily modified cellular tRNAs and the unmodified or the lightly modified mitochondrial tRNAs (mt-tRNA). We find that both a T7 transcript of yeast tRNA(Phe) and natively extracted total bovine liver mt-tRNA activate PKR in vitro, whereas native E. coli, bovine liver, yeast, and wheat tRNA(Phe) do not, nor do a variety of base- or sugar-modified T7 transcripts. These results are further supported by activation of PKR by a natively folded T7 transcript of tRNA(Phe)in vivo supporting the importance of tRNA modification in suppressing PKR activation in cells. We also examine PKR activation by a T7 transcript of the A14G pathogenic mutant of mt-tRNA(Leu), which is known to dimerize, and find that the misfolded dimeric form activates PKR in vitro while the monomeric form does not. Overall, the in vitro and in vivo findings herein indicate that tRNAs have an intrinsic ability to activate PKR and that nucleoside modifications and native RNA tertiary folding may function, at least in part, to suppress such activation, thus serving to distinguish self and non-self tRNA in innate immunity.
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Affiliation(s)
- Subba Rao Nallagatla
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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10
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Giegé R. Fifty years excitement with science: recollections with and without tRNA. J Biol Chem 2013; 288:6679-87. [PMID: 23325807 DOI: 10.1074/jbc.x113.453894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 67084 Strasbourg, France.
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11
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Biro JC, Biro JM. The concept of RNA-assisted protein folding: Representation of amino acid kinetics at the tRNA level. J Theor Biol 2013; 317:168-74. [DOI: 10.1016/j.jtbi.2012.09.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
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12
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Biro JC. The concept of RNA-assisted protein folding: the role of tRNA. Theor Biol Med Model 2012; 9:10. [PMID: 22462735 PMCID: PMC3359187 DOI: 10.1186/1742-4682-9-10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 04/02/2012] [Indexed: 02/07/2023] Open
Abstract
We suggest that tRNA actively participates in the transfer of 3D information from mRNA to peptides--in addition to its well-known, "classical" role of translating the 3-letter RNA codes into the one letter protein code. The tRNA molecule displays a series of thermodynamically favored configurations during translation, a movement which places the codon and coded amino acids in proximity to each other and make physical contact between some amino acids and their codons possible. This specific codon-amino acid interaction of some selected amino acids is necessary for the transfer of spatial information from mRNA to coded proteins, and is known as RNA-assisted protein folding.
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Affiliation(s)
- Jan C Biro
- Karolinska Institute, Stockholm, Sweden.
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13
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Ali OY, Randell NM, Fridgen TD. Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]+ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO. Chemphyschem 2012; 13:1507-13. [DOI: 10.1002/cphc.201200015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/07/2012] [Indexed: 11/07/2022]
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14
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Bhaskaran H, Rodriguez-Hernandez A, Perona JJ. Kinetics of tRNA folding monitored by aminoacylation. RNA (NEW YORK, N.Y.) 2012; 18:569-80. [PMID: 22286971 PMCID: PMC3285943 DOI: 10.1261/rna.030080.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/23/2011] [Indexed: 05/20/2023]
Abstract
We describe a strategy for tracking Mg²⁺-initiated folding of ³²P-labeled tRNA molecules to their native structures based on the capacity for aminoacylation by the cognate aminoacyl-tRNA synthetase enzyme. The approach directly links folding to function, paralleling a common strategy used to study the folding of catalytic RNAs. Incubation of unfolded tRNA with magnesium ions, followed by the addition of aminoacyl-tRNA synthetase and further incubation, yields a rapid burst of aminoacyl-tRNA formation corresponding to the prefolded tRNA fraction. A subsequent slower increase in product formation monitors continued folding in the presence of the enzyme. Further analysis reveals the presence of a parallel fraction of tRNA that folds more rapidly than the majority of the population. The application of the approach to study the influence of post-transcriptional modifications in folding of Escherichia coli tRNA₁(Gln) reveals that the modified bases increase the folding rate but do not affect either the equilibrium between properly folded and misfolded states or the folding pathway. This assay allows the use of ³²P-labeled tRNA in integrated studies combining folding, post-transcriptional processing, and aminoacylation reactions.
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Affiliation(s)
| | | | - John J. Perona
- Department of Chemistry and Biochemistry
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
- Corresponding author.E-mail .
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15
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Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Suga K, Tanabe T, Tomita H, Shimanouchi T, Umakoshi H. Conformational change of single-stranded RNAs induced by liposome binding. Nucleic Acids Res 2011; 39:8891-900. [PMID: 21785134 PMCID: PMC3203612 DOI: 10.1093/nar/gkr568] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The interaction between single-stranded RNAs and liposomes was studied using UV, Fourier Transform Infrared spectroscopy (FTIR) and Circular Dichroism spectroscopy (CD). The effect of the surface characteristics of liposomes, which were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and modified with cholesterol (Ch) or 1,2-dioleoyl-3-trimethylammonium propane (DOTAP), on the liposome–RNA interaction was investigated. The fluorescence of 6-(p-toluidino)naphthalene-2-sulfonate (TNS) embedded in the liposome surface (ε = 30–40) was decreased in the presence of tRNA, suggesting that single-stranded tRNA could bind onto the liposome. The dehydration of –PO2− –, guanine (G) and cytosine (C) of tRNA molecules in the presence of liposomes suggested both an electrostatic interaction (phosphate backbone of tRNA and trimethylammonium group of POPC, DOTAP) and a hydrophobic interaction (guanine or cytosine of tRNA and aliphatic tail of lipid). The tRNA conformation on the liposome was determined by CD spectroscopy. POPC/Ch (70/30) maintained tRNA conformation without any denaturation, while POPC/DOTAP(70/30) drastically denatured it. The mRNA translation was evaluated in an Escherichia coli cell-free translation system. POPC/Ch(70/30) enhanced expression of green fluorescent protein (GFP) (116%) while POPC/DOTAP(70/30) inhibited (37%), suggesting that the conformation of RNAs was closely related to the translation efficiency. Therefore, single-stranded RNAs could bind to liposomal membranes through electrostatic and hydrophobic attraction, after which conformational changes were induced depending on the liposome characteristics.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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17
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Pearson D, Carell T. Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm5s2U to mnm5s2U. Nucleic Acids Res 2011; 39:4818-26. [PMID: 21306992 PMCID: PMC3113582 DOI: 10.1093/nar/gkr071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transfer RNA (tRNA) contains a number of complex ‘hypermodified’ nucleosides that are essential for a number of genetic processes. Intermediate forms of these nucleosides are rarely found in tRNA despite the fact that modification is not generally a complete process. We propose that the modification machinery is tuned into an efficient ‘assembly line’ that performs the modification steps at similar, or sequentially increasing, rates to avoid build-up of possibly deleterious intermediates. To investigate this concept, we measured steady-state kinetics for the final two steps of the biosynthesis of the mnm5s2U nucleoside in Escherichia coli tRNAGlu, which are both catalysed by the bifunctional MnmC enzyme. High-performance liquid chromatography-based assays using selectively under-modified tRNA substrates gave a Km value of 600 nM and kcat 0.34 s−1 for the first step, and Km 70 nM and kcat 0.31 s−1 for the second step. These values show that the second reaction occurs faster than the first reaction, or at a similar rate at very high substrate concentrations. This result indicates that the enzyme is kinetically tuned to produce fully modified mnm5(s2)U while avoiding build-up of the nm5(s2)U intermediate. The assay method developed here represents a general approach for the comparative analysis of tRNA-modifying enzymes.
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Affiliation(s)
- David Pearson
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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18
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Abstract
RNAs and RNA-protein complexes (RNPs) traverse rugged energy landscapes as they fold to their native structures, and many continue to undergo conformational rearrangements as they function. Due to the inherent stability of local RNA structure, proteins are required to assist with RNA conformational transitions during initial folding and in exchange between functional structures. DEAD-box proteins are superfamily 2 RNA helicases that are ubiquitously involved in RNA-mediated processes. Some of these proteins use an ATP-dependent cycle of conformational changes to disrupt RNA structure nonprocessively, accelerating structural transitions of RNAs and RNPs in a manner that bears a strong resemblance to the activities of certain groups of protein chaperones. This review summarizes recent work using model substrates and tractable self-splicing intron RNAs, which has given new insights into how DEAD-box proteins promote RNA folding steps and conformational transitions, and it summarizes recent progress in identifying sites and mechanisms of DEAD-box protein activity within more complex cellular targets.
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Affiliation(s)
- Cynthia Pan
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX, USA
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19
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Suga K, Umakoshi H, Tomita H, Tanabe T, Shimanouchi T, Kuboi R. Liposomes destabilize tRNA during heat stress. Biotechnol J 2010; 5:526-9. [PMID: 20401904 DOI: 10.1002/biot.200900289] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Biomembranes play an important role in cellular response to heat stress. In this study, we focus on the interaction between liposomes and tRNA. Upon heat treatment we determined circular dichroism spectra of tRNA in presence of liposomes prepared from POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and cholesterol (Ch). To compare thermal stability, midpoint temperature (T(m)) of tRNA was calculated from normalized theta(208). Addition of POPC/Ch liposomes decreased the T(m) value of tRNA from 48 degrees C to 38 degrees C. We conclude that POPC/Ch liposomes interact with tRNA and destabilize its conformation under heat stress.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka, Japan
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20
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Kolesnikova O, Kazakova H, Comte C, Steinberg S, Kamenski P, Martin RP, Tarassov I, Entelis N. Selection of RNA aptamers imported into yeast and human mitochondria. RNA (NEW YORK, N.Y.) 2010; 16:926-941. [PMID: 20348443 PMCID: PMC2856887 DOI: 10.1261/rna.1914110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 02/01/2010] [Indexed: 05/29/2023]
Abstract
In the yeast Saccharomyces cerevisiae, nuclear DNA-encoded is partially imported into mitochondria. We previously found that the synthetic transcripts of yeast tRNA(Lys) and a number of their mutant versions could be specifically internalized by isolated yeast and human mitochondria. The mitochondrial targeting of tRNA(Lys) in yeast was shown to depend on the cytosolic precursor of mitochondrial lysyl-tRNA synthetase and the glycolytic enzyme enolase. Here we applied the approach of in vitro selection (SELEX) to broaden the spectrum of importable tRNA-derived molecules. We found that RNAs selected for their import into isolated yeast mitochondria have lost the potential to acquire a classical tRNA-shape. Analysis of conformational rearrangements in the importable RNAs by in-gel fluorescence resonance energy transfer (FRET) approach permitted us to suggest that protein factor binding and subsequent import require formation of an alternative structure, different from a classic L-form tRNA model. We show that in the complex with targeting protein factor, enolase 2, tRK1 adopts a particular conformation characterized by bringing together the 3'-end and the TPsiC loop. This is a first evidence for implication of RNA secondary structure rearrangement in the mechanism of mitochondrial import selectivity. Based on these data, a set of small RNA molecules with significantly improved efficiency of import into yeast and human mitochondria was constructed, opening the possibility of creating a new mitochondrial vector system able to target therapeutic oligoribonucleotides into deficient human mitochondria.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Biological Transport, Active
- Fluorescence Resonance Energy Transfer
- Humans
- In Vitro Techniques
- Lysine-tRNA Ligase/metabolism
- Mitochondria/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phosphopyruvate Hydratase/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- SELEX Aptamer Technique
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Olga Kolesnikova
- UMR 7156, Université de Strasbourg/Centre National de la Recherche Scientifique (UdS/CNRS), 67084 Strasbourg, France
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21
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Oliva R, Cavallo L. Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs. J Phys Chem B 2010; 113:15670-8. [PMID: 19921955 DOI: 10.1021/jp906847p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed MP2 calculations to elucidate the structure and energetics of the Mg(2+), Mn(2+), and Co(2+) hexahydrated aquaions, and the effect of the metal binding to the N7 atom of (i) a single guanine, (ii) a guanine involved in a Watson-Crick pair, and (iii) a guanine involved in a reverse Watson-Crick base pair. Our comparative analysis of the three aquaions indicates a clear inverse correlation between the radius of the cation and the binding energy, that indeed increases in the order Mn(2+) < Co(2+) < Mg(2+). The trend in the binding energies of the pentahydrated cations to the N7 atom of the guanine is instead Mg(2+) < Mn(2+) < Co(2+), suggesting a rather different bonding scheme that, for the two transition metals, involves back-donation from the aromatic ring of the guanine to their empty d orbitals. In the gas phase, the three hydrated metals significantly stabilize both G-C base pair geometries, Watson-Crick and reverse Watson-Crick, we investigated. Inclusion of a continuous solvent model, however, remarkably reduces this additional stabilization, which becomes almost negligible in the case of the Mg(2+) cation coordinated to the guanine in the standard Watson-Crick geometry. Conversely, all three metal ions sensibly stabilize the reverse Watson-Crick geometry, also in water. Our results are supported by a screening of the structures available in the Protein Data Bank, which clearly indicates that the two transition metals we investigated have a tendency greater than Mg(2+) to coordinate to the N7 atom of guanines, and that there is no clear correlation between the number of guanines in experimental structures with a metal bound to N7 atom and their involvement in Watson-Crick base pairs.
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Affiliation(s)
- Romina Oliva
- Dipartimento di Scienze Applicate, Università di Napoli Parthenope, I-80143 Naples, Italy
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22
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Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JWS, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (NEW YORK, N.Y.) 2009; 15:2147-60. [PMID: 19850906 PMCID: PMC2779667 DOI: 10.1261/rna.1738409] [Citation(s) in RCA: 465] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA(Gln) is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro.
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Affiliation(s)
- Christian Cole
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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23
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The dimeric proto-ribosome: Structural details and possible implications on the origin of life. Int J Mol Sci 2009; 10:2921-2934. [PMID: 19742176 PMCID: PMC2738903 DOI: 10.3390/ijms10072921] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/25/2009] [Indexed: 11/16/2022] Open
Abstract
A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. This structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. By catalyzing the production of random peptide chains, the proto-ribosome could have enabled the formation of primary enzymes, launching a process of co-evolution of the translation apparatus and the proteins, thus presenting an alternative to the RNA world hypothesis.
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24
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Abstract
RNA folds to a myriad of three-dimensional structures and performs an equally diverse set of functions. The ability of RNA to fold and function in vivo is all the more remarkable because, in vitro, RNA has been shown to have a strong propensity to adopt misfolded, non-functional conformations. A principal factor underlying the dominance of RNA misfolding is that local RNA structure can be quite stable even in the absence of enforcing global tertiary structure. This property allows non-native structure to persist, and it also allows native structure to form and stabilize non-native contacts or non-native topology. In recent years it has become clear that one of the central reasons for the apparent disconnect between the capabilities of RNA in vivo and its in vitro folding properties is the presence of RNA chaperones, which facilitate conformational transitions of RNA and therefore mitigate the deleterious effects of RNA misfolding. Over the past two decades, it has been demonstrated that several classes of non-specific RNA binding proteins possess profound RNA chaperone activity in vitro and when overexpressed in vivo, and at least some of these proteins appear to function as chaperones in vivo. More recently, it has been shown that certain DExD/H-box proteins function as general chaperones to facilitate folding of group I and group II introns. These proteins are RNA-dependent ATPases and have RNA helicase activity, and are proposed to function by using energy from ATP binding and hydrolysis to disrupt RNA structure and/or to displace proteins from RNA-protein complexes. This review outlines experimental studies that have led to our current understanding of the range of misfolded RNA structures, the physical origins of RNA misfolding, and the functions and mechanisms of putative RNA chaperone proteins.
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Affiliation(s)
- Rick Russell
- Department of Chemistry and Biochemistry, The Institute For Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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25
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Oliva R, Tramontano A, Cavallo L. Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA (NEW YORK, N.Y.) 2007; 13:1427-36. [PMID: 17652139 PMCID: PMC1950755 DOI: 10.1261/rna.574407] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The G15-C48 Levitt base pair, located at a crucial position in the core of canonical tRNAs, assumes a reverse Watson-Crick (RWC) geometry. By means of bioinformatics analysis and quantum mechanics calculations we show here that such a geometry is moderately more stable than an alternative bifurcated trans geometry, involving the guanine Watson-Crick face and the cytosine keto group, which we have also found in known RNA structures. However we also demonstrate that the RWC geometry can take advantage of additional stabilizing effects such as metal binding or post-transcriptional chemical modification. One of the few strong metal binding sites characterized for cytosolic tRNAs is localized on G15, and a domain-specific complex modification known as archaeosine is widespread at position 15 in archaeal tRNAs. We have found that both the bound Mg2+ ion and the archaeosine modification induce an analogous electron density redistribution, which results in an effective stabilization of the RWC geometry. Metal binding and chemical modification thus play an interchangeable role in stabilizing the G15-C48 correct geometry. Interestingly, these different but convergent strategies are selectively adopted in the different life domains.
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Affiliation(s)
- Romina Oliva
- Dipartimento di Scienze Applicate, Università di Napoli Parthenope, Naples, Italy.
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26
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Crozier SP, Garner HR. Ensemble-based RNA secondary structure characterization. IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE : THE QUARTERLY MAGAZINE OF THE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY 2007; 26:72-86. [PMID: 17278775 DOI: 10.1109/memb.2007.289125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Stephen P Crozier
- University of Texas Southwestern Medical Center, Dallas, 75390, USA.
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27
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Roy MD, Wittenhagen LM, Kelley SO. Structural probing of a pathogenic tRNA dimer. RNA (NEW YORK, N.Y.) 2005; 11:254-260. [PMID: 15701731 PMCID: PMC1370715 DOI: 10.1261/rna.7143305] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Accepted: 12/09/2004] [Indexed: 05/24/2023]
Abstract
The A3243G mutation within the human mitochondrial (hs mt) tRNALeuUUR gene is associated with maternally inherited deafness and diabetes (MIDD) and other mitochondrial encephalopathies. One of the most pronounced structural effects of this mutation is the disruption of the native structure through stabilization of a high-affinity dimeric complex. We conducted a series of studies that address the structural properties of this tRNA dimer, and we assessed its formation under physiological conditions. Enzymatic probing was used to directly define the dimeric interface for the complex, and a discrete region of the D-stem and loop of hs mt tRNALeuUUR was identified. The dependence of dimerization on magnesium ions and temperature was also tested. The formation of the tRNA dimer is influenced by temperature, with dimerization becoming more efficient at physiological temperature. Complexation of the mutant tRNA is also affected by the amount of magnesium present, and occurs at concentrations present intracellularly. Terbium probing experiments revealed a specific metal ion-binding site localized at the site of the A3243G mutation that is unique to the dimer structure. This metal ion-binding site presents a striking parallel to dimeric complexes of viral RNAs, which use the same hexanucleotide sequence for complexation and feature a similarly positioned metal ion-binding site within the dimeric structure. Taken together, these results indicate that the unique dimeric complex formed by the hs mt tRNALeuUUR A3243G mutant exhibits interesting similarities to biological RNA dimers, and may play a role in the loss of function caused by this mutation in vivo.
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Affiliation(s)
- Marc D Roy
- Boston College, Eugene F. Merkert Chemistry Center, Chestnut Hill, MA 02467, USA
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28
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Banerjee R, Mandal AK, Saha R, Guha S, Samaddar S, Bhattacharyya A, Roy S. Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases. Nucleic Acids Res 2004; 31:6035-42. [PMID: 14530451 PMCID: PMC219465 DOI: 10.1093/nar/gkg779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Discrimination between cognate and non-cognate tRNAs by aminoacyl-tRNA synthetases occurs at several steps of the aminoacylation pathway. We have measured changes of solvation and counter-ion distribution at various steps of the aminoacylation pathway of glutamyl- and glutaminyl-tRNA synthetases. The decrease in the association constant with increasing KCl concentration is relatively small for cognate tRNA binding when compared to known DNA-protein interactions. The electro-neutral nature of the tRNA binding domain may be largely responsible for this low ion release stoichiometry, suggesting that a relatively large electrostatic component of the DNA-protein interaction free energy may have evolved for other purposes, such as, target search. Little change in solvation upon tRNA binding is seen. Non-cognate tRNA binding actually increases with increasing KCl concentration indicating that charge repulsion may be a significant component of binding free energy. Thus, electrostatic interactions may have been used to discriminate between cognate and non-cognate tRNAs in the binding step. The catalytic constant of glutaminyl-tRNA synthetase increases with increasing osmotic pressure indicating a water release of 8.4 +/- 1.4 mol/mol in the transition state, whereas little change is seen in the case of glutamyl-tRNA synthetase. We propose that the significant amount of water release in the transition state, in the case of glutaminyl-tRNA synthetase, is due to additional contact of the protein with the tRNA in the transition state.
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Affiliation(s)
- Rajat Banerjee
- Department of Biophysics, Bose Institute, P-1/12, C.I.T. Scheme VII M, Calcutta 700 054, India
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29
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Vanathi P, Mishra AK, Bhargava P. Regulation of activity of the yeast TATA-binding protein through intra-molecular interactions. J Biosci 2003; 28:413-21. [PMID: 12799488 DOI: 10.1007/bf02705116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Dimerization is proposed to be a regulatory mechanism for TATA-binding protein (TBP) activity both in vitro and in vivo. The reversible dimer-monomer transition of TBP is influenced by the buffer conditions in vitro. Using in vitro chemical cross-linking, we found yeast TBP (yTBP) to be largely monomeric in the presence of the divalent cation Mg2+, even at high salt concentrations. Apparent molecular mass of yTBP at high salt with Mg2+, run through a gel filtration column, was close to that of monomeric yTBP. Lowering the monovalent ionic concentration in the absence of Mg2+, resulted in dimerization of TBP. Effect of Mg2+ was seen at two different levels: at higher TBP concentrations, it suppressed the TBP dimerization and at lower TBP levels, it helped keep TBP monomers in active conformation (competent for binding TATA box), resulting in enhanced TBP-TATA complex formation in the presence of increasing Mg2+. At both the levels, activity of the full-length TBP in the presence of Mg2+ was like that reported for the truncated C-terminal domain of TBP from which the N-terminus is removed. Therefore for full-length TBP, intra-molecular interactions can regulate its activity via a similar mechanism.
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Affiliation(s)
- Perumal Vanathi
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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30
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Höbartner C, Ebert MO, Jaun B, Micura R. RNA Two-State Conformation Equilibria and the Effect of Nucleobase Methylation. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3773(20020215)41:4<605::aid-anie605>3.0.co;2-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Höbartner C, Ebert MO, Jaun B, Micura R. RNA-Konformationsgleichgewichte und der Einfluss der Methylierung von Nucleobasen auf die Gleichgewichtslage. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3757(20020215)114:4<619::aid-ange619>3.0.co;2-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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