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Journal articles on the topic 'TRNA Structure'

Author: Grafiati

Published: 6 September 2023

Last updated: 7 September 2023

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1

Fiteha, Yosur G., and Mahmoud Magdy. "The Evolutionary Dynamics of the Mitochondrial tRNA in the Cichlid Fish Family." Biology 11, no. 10 (2022): 1522. http://dx.doi.org/10.3390/biology11101522.

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The mitochondrial transfer RNA genes (tRNAs) attract more attention due to their highly dynamic and rapidly evolving nature. The current study aimed to detect and evaluate the dynamics, characteristic patterns, and variations of mitochondrial tRNAs. The study was conducted in two main parts: first, the published mitogenomic sequences of cichlids mt tRNAs have been filtered. Second, the filtered mitochondrial tRNA and additional new mitogenomes representing the most prevalent Egyptian tilapiine were compared and analyzed. Our results revealed that all 22 tRNAs of cichlids folded into a classica

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2

Urbonavičius, Jaunius, Jérôme M. B. Durand, and Glenn R. Björk. "Three Modifications in the D and T Arms of tRNA Influence Translation in Escherichia coli and Expression of Virulence Genes in Shigella flexneri." Journal of Bacteriology 184, no. 19 (2002): 5348–57. http://dx.doi.org/10.1128/jb.184.19.5348-5357.2002.

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ABSTRACT The modified nucleosides 2′-O-methylguanosine, present at position 18 (Gm18), 5-methyluridine, present at position 54 (m5U54), and pseudouridine, present at position 55 (Ψ55), are located in the D and T arms of tRNAs and are close in space in the three-dimensional (3D) structure of this molecule in the bacterium Escherichia coli. The formation of these modified nucleosides is catalyzed by the products of genes trmH (Gm18), trmA (m5U54), and truB (Ψ55). The combination of trmH, trmA, and truB mutations resulting in lack of these three modifications reduced the growth rate, especially a

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3

Mangroo, Dev, Xin-Qi Wu, and Uttam L. Rajbhandary. "Escherichia coliinitiator tRNA: structure–function relationships and interactions with the translational machinery." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1023–31. http://dx.doi.org/10.1139/o95-109.

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We showed previously that the sequence and (or) structural elements important for specifying the many distinctive properties of Escherichia coli initiator tRNA are clustered in the acceptor stem and in the anticodon stem and loop. This paper briefly describes this and reviews the results of some recently published studies on the mutant initiator tRNAs generated during this work. First, we have studied the effect of overproduction of methionyl-tRNA transformylase (MTF) and initiation factors IF2 and IF3 on activity of mutant initiator tRNAs mat are defective at specific steps in the initiation

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4

Teramoto, Takamasa, Kipchumba J. Kaitany, Yoshimitsu Kakuta, Makoto Kimura, Carol A. Fierke, and Traci M. Tanaka Hall. "Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA." Nucleic Acids Research 48, no. 21 (2020): 11815–26. http://dx.doi.org/10.1093/nar/gkaa627.

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Abstract Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5′-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNA

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5

Chiang, C. C., and A. M. Lambowitz. "The Mauriceville retroplasmid reverse transcriptase initiates cDNA synthesis de novo at the 3' end of tRNAs." Molecular and Cellular Biology 17, no. 8 (1997): 4526–35. http://dx.doi.org/10.1128/mcb.17.8.4526.

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The Mauriceville retroplasmid of Neurospora mitochondria encodes a novel reverse transcriptase that initiates cDNA synthesis de novo (i.e., without a primer) at the 3' CCA of the plasmid transcript's 3' tRNA-like structure (H. Wang and A. M. Lambowitz, Cell 75:1071-1081, 1993). Here, we show that the plasmid reverse transcriptase also initiates cDNA synthesis de novo at the 3' end of tRNAs, leading to synthesis of a full-length cDNA copy of the tRNA. The use of tRNA templates in vivo was suggested previously by the structure of suppressive mutant plasmids that have incorporated mitochondrial t

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6

Nakamura, Akiyoshi, Taiki Nemoto, Isao Tanaka, and Min Yao. "Structural analysis of tRNA(His) guanylyltransferase comlexed with tRNA." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1816. http://dx.doi.org/10.1107/s2053273314081844.

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tRNA(His) guanylyltransferase (Thg1) of eukaryote adds a guanylate to the 5' end of immature or incorrectly processed tRNAs (3'-5' polymerization) by three reaction steps: adenylylation; guanylylation and dephosphorylation. This additional guanylate provides the major identity element for histidyl-tRNA synthetase to recognize its cognate substrate tRNA(His) and differentiates tRNA(His) from the pool of tRNAs present in the cell (1). Previous studies indicate that Thg1 is a structural homolog of canonical 5'-3' polymerases in the catalytic core with no obvious conservation of the amino acid seq

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7

Hòa, Lê Thanh, Nguyễn Thị Khuê, Nguyễn Thị Bích Nga, et al. "Genetic characterization of mitochondrial genome of the small intestinal fluke, Haplorchis taichui (Trematoda: Heterophyidae), Vietnamese sample." Vietnam Journal of Biotechnology 14, no. 2 (2016): 215–24. http://dx.doi.org/10.15625/1811-4989/14/2/9333.

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The small intestinal fluke, Haplorchis taichui Nishigori, 1924, belonging to genus Haplorchis (family Heterophyidae, class Trematoda, phylum Platyhelminthes), is a zoonotic pathogen causing disease in humans and animals. Complete mitochondrial genome (mtDNA) of H. taichui (strain HTAQT, collected from Quang Tri) was obtained and characterized for structural genomics providing valuable data for studies on epidemiology, species identification, diagnosis, classification, molecular phylogenetic relationships and prevention of the disease. The entire nucleotide mtDNA sequence of H. taichui (HTAQT)

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8

Ramos-Morales, Elizabeth, Efil Bayam, Jordi Del-Pozo-Rodríguez, et al. "The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination." Nucleic Acids Research 49, no. 11 (2021): 6529–48. http://dx.doi.org/10.1093/nar/gkab436.

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Abstract Post-transcriptional modification of tRNA wobble adenosine into inosine is crucial for decoding multiple mRNA codons by a single tRNA. The eukaryotic wobble adenosine-to-inosine modification is catalysed by the ADAT (ADAT2/ADAT3) complex that modifies up to eight tRNAs, requiring a full tRNA for activity. Yet, ADAT catalytic mechanism and its implication in neurodevelopmental disorders remain poorly understood. Here, we have characterized mouse ADAT and provide the molecular basis for tRNAs deamination by ADAT2 as well as ADAT3 inactivation by loss of catalytic and tRNA-binding determ

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9

O'Donoghue, Patrick, and Zaida Luthey-Schulten. "On the Evolution of Structure in Aminoacyl-tRNA Synthetases." Microbiology and Molecular Biology Reviews 67, no. 4 (2003): 550–73. http://dx.doi.org/10.1128/mmbr.67.4.550-573.2003.

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SUMMARY The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. The evolution of the tRNA synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an RNA world to the modern world dominated by protein-enzymes. We present a structure-based phylogeny of the aminoacyl-tRNA synthetases. By using structural alignments of all of the aminoacyl-tRNA synthetases of

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10

Strobel, M. C., and J. Abelson. "Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo." Molecular and Cellular Biology 6, no. 7 (1986): 2663–73. http://dx.doi.org/10.1128/mcb.6.7.2663-2673.1986.

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The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base

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11

Strobel, M. C., and J. Abelson. "Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo." Molecular and Cellular Biology 6, no. 7 (1986): 2663–73. http://dx.doi.org/10.1128/mcb.6.7.2663.

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The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base

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12

BYKHOVSKI, ALEXEI, TATIANA GLOBUS, TATYANA KHROMOVA, BORIS GELMONT, and DWIGHT WOOLARD. "AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS." International Journal of High Speed Electronics and Systems 17, no. 02 (2007): 225–37. http://dx.doi.org/10.1142/s012915640700445x.

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The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated an

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13

Kawabata, Mai, Kentaro Kawashima, Hiromi Mutsuro-Aoki, Tadashi Ando, Takuya Umehara, and Koji Tamura. "Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center." Life 12, no. 4 (2022): 573. http://dx.doi.org/10.3390/life12040573.

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The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis dep

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14

Cummins, C. M., M. R. Culbertson, and G. Knapp. "Frameshift suppressor mutations outside the anticodon in yeast proline tRNAs containing an intervening sequence." Molecular and Cellular Biology 5, no. 7 (1985): 1760–71. http://dx.doi.org/10.1128/mcb.5.7.1760-1771.1985.

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Extragenic suppressors of +1 frameshift mutations in proline codons map in genes encoding two major proline tRNA isoacceptors. We have shown previously that one isoacceptor encoded by the SUF2 gene (chromosome 3) contains no intervening sequence. SUF2 suppressor mutations result from the base insertion of a G within a 3'-GGA-5' anticodon, allowing the tRNA to read a 4-base code word. In this communication we describe suppressor mutations in genes encoding a second proline tRNA isoacceptor (wild-type anticodon 3'-GGU-5') that result in a novel mechanism for translation of a 4-base genetic code

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15

Cummins, C. M., M. R. Culbertson, and G. Knapp. "Frameshift suppressor mutations outside the anticodon in yeast proline tRNAs containing an intervening sequence." Molecular and Cellular Biology 5, no. 7 (1985): 1760–71. http://dx.doi.org/10.1128/mcb.5.7.1760.

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Extragenic suppressors of +1 frameshift mutations in proline codons map in genes encoding two major proline tRNA isoacceptors. We have shown previously that one isoacceptor encoded by the SUF2 gene (chromosome 3) contains no intervening sequence. SUF2 suppressor mutations result from the base insertion of a G within a 3'-GGA-5' anticodon, allowing the tRNA to read a 4-base code word. In this communication we describe suppressor mutations in genes encoding a second proline tRNA isoacceptor (wild-type anticodon 3'-GGU-5') that result in a novel mechanism for translation of a 4-base genetic code

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16

Wang, S. S., and A. K. Hopper. "Isolation of a yeast gene involved in species-specific pre-tRNA processing." Molecular and Cellular Biology 8, no. 12 (1988): 5140–49. http://dx.doi.org/10.1128/mcb.8.12.5140-5149.1988.

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To identify genes involved in pre-tRNA processing, we searched for yeast DNA sequences that specifically enhanced the expression of the SUP4(G37) gene. The SUP4(G37) gene possesses a point mutation at position 37 of suppressor tRNA(Tyr). This lesion results in a reduced rate of pre-tRNA splicing and a decreased level of nonsense suppression. A SUP4(G37) strain was transformed with a yeast genomic library, and the transformants were screened for increased suppressor activity. One transformant contained a plasmid that encoded an unessential gene, STP1, that in multiple copies enhanced the suppre

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17

Wang, S. S., and A. K. Hopper. "Isolation of a yeast gene involved in species-specific pre-tRNA processing." Molecular and Cellular Biology 8, no. 12 (1988): 5140–49. http://dx.doi.org/10.1128/mcb.8.12.5140.

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To identify genes involved in pre-tRNA processing, we searched for yeast DNA sequences that specifically enhanced the expression of the SUP4(G37) gene. The SUP4(G37) gene possesses a point mutation at position 37 of suppressor tRNA(Tyr). This lesion results in a reduced rate of pre-tRNA splicing and a decreased level of nonsense suppression. A SUP4(G37) strain was transformed with a yeast genomic library, and the transformants were screened for increased suppressor activity. One transformant contained a plasmid that encoded an unessential gene, STP1, that in multiple copies enhanced the suppre

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18

Caulfield, Thomas R., Batsal Devkota, and Geoffrey C. Rollins. "Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data." Journal of Biophysics 2011 (March 28, 2011): 1–11. http://dx.doi.org/10.1155/2011/219515.

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We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may

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19

Akins, R. A., R. L. Kelley, and A. M. Lambowitz. "Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription." Molecular and Cellular Biology 9, no. 2 (1989): 678–91. http://dx.doi.org/10.1128/mcb.9.2.678-691.1989.

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The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the positio

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20

Akins, R. A., R. L. Kelley, and A. M. Lambowitz. "Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription." Molecular and Cellular Biology 9, no. 2 (1989): 678–91. http://dx.doi.org/10.1128/mcb.9.2.678.

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The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the positio

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21

Qi, Fangbing, Yajing Zhao, Ningbo Zhao, Kai Wang, Zhonghu Li, and Yingjuan Wang. "Structural variation and evolution of chloroplast tRNAs in green algae." PeerJ 9 (June 1, 2021): e11524. http://dx.doi.org/10.7717/peerj.11524.

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As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ra

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22

Kelly, Nathan J., та Casey D. Morrow. "Structural Elements of the tRNA TΨC Loop Critical for Nucleocytoplasmic Transport Are Important for Human Immunodeficiency Virus Type 1 Primer Selection". Journal of Virology 79, № 10 (2005): 6532–39. http://dx.doi.org/10.1128/jvi.79.10.6532-6539.2005.

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ABSTRACT Human immunodeficiency virus type 1 (HIV-1) selects a host cell tRNA as the primer for the initiation of reverse transcription. In a previous study, transport of the intact tRNA from the nucleus to the cytoplasm during tRNA biogenesis was shown to be a requirement for the selection of the tRNA primer by HIV-1. To further examine the importance of tRNA structure for transport and the selection of the primer, yeast tRNAPhe mutants were designed such that the native tRNA structure would be disrupted to various extents. The capacity of the mutant tRNAPhe to complement a defective HIV-1 pr

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23

Florentz, Catherine. "Molecular Investigations on tRNAs Involved in Human Mitochondrial Disorders." Bioscience Reports 22, no. 1 (2002): 81–98. http://dx.doi.org/10.1023/a:1016065107165.

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Over the last decade, human neurodegenerative disorders which correlate with point mutations in mitochondrial tRNA genes became more and more numerous. Both the number of mutations (more than 70) and the variety of phenotypes (cardiopathies, myopathies, encephalopathies as well as diabetes, deafness or others) render the understanding of the genotype/phenotype relationships very complex. Here we first summarize the efforts undertaken to decipher the initial impact of various mutations on the structure/function relationships of tRNAs. This includes several lines of research, namely (i) investig

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24

Lin, Brian Y., Patricia P. Chan, and Todd M. Lowe. "tRNAviz: explore and visualize tRNA sequence features." Nucleic Acids Research 47, W1 (2019): W542—W547. http://dx.doi.org/10.1093/nar/gkz438.

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Abstract Transfer RNAs (tRNAs) are ubiquitous across the tree of life. Although tRNA structure is highly conserved, there is still significant variation in sequence features between clades, isotypes and even isodecoders. This variation not only impacts translation, but as shown by a variety of recent studies, nontranslation-associated functions are also sensitive to small changes in tRNA sequence. Despite the rapidly growing number of sequenced genomes, there is a lack of tools for both small- and large-scale comparative genomics analysis of tRNA sequence features. Here, we have integrated ove

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25

Ito, Takuhiro, Noriko Kiyasu, Risa Matsunaga, Seizo Takahashi, and Shigeyuki Yokoyama. "Structure of nondiscriminating glutamyl-tRNA synthetase fromThermotoga maritima." Acta Crystallographica Section D Biological Crystallography 66, no. 7 (2010): 813–20. http://dx.doi.org/10.1107/s0907444910019086.

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Aminoacyl-tRNA synthetases produce aminoacyl-tRNAs from the substrate tRNA and its cognate amino acid with the aid of ATP. Two types of glutamyl-tRNA synthetase (GluRS) have been discovered: discriminating GluRS (D-GluRS) and nondiscriminating GluRS (ND-GluRS). D-GluRS glutamylates tRNAGluonly, while ND-GluRS glutamylates both tRNAGluand tRNAGln. ND-GluRS produces the intermediate Glu-tRNAGln, which is converted to Gln-tRNAGlnby Glu-tRNAGlnamidotransferase. Two GluRS homologues fromThermotoga maritima, TM1875 and TM1351, have been biochemically characterized and it has been clarified that only

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Ito, Takuhiro, Isao Masuda, Ken-ichi Yoshida, et al. "Structural basis for methyl-donor–dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD." Proceedings of the National Academy of Sciences 112, no. 31 (2015): E4197—E4205. http://dx.doi.org/10.1073/pnas.1422981112.

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The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in transfer RNAs (tRNAs) with the 36GG37 sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revea

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Grigg, Jason C., Ian R. Price, and Ailong Ke. "tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch." Crystals 12, no. 5 (2022): 694. http://dx.doi.org/10.3390/cryst12050694.

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RNAs are prone to misfolding and are often more challenging to crystallize and phase than proteins. Here, we demonstrate that tRNA fusion can streamline the crystallization and structure determination of target RNA molecules. This strategy was applied to the T-box riboswitch system to capture a dynamic interaction between the tRNA 3′-UCCA tail and the T-box antiterminator, which senses aminoacylation. We fused the T-box antiterminator domain to the tRNA anticodon arm to capture the intended interaction through crystal packing. This approach drastically improved the probability of crystallizati

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Ding, Yu, Beibei Gao, and Jinyu Huang. "Mitochondrial Cardiomyopathy: The Roles of mt-tRNA Mutations." Journal of Clinical Medicine 11, no. 21 (2022): 6431. http://dx.doi.org/10.3390/jcm11216431.

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Mitochondria are important organelles whose primary role is generating energy through the oxidative phosphorylation (OXPHOS) system. Cardiomyopathy, a common clinical disorder, is frequently associated with pathogenic mutations in nuclear and mitochondrial genes. To date, a growing number of nuclear gene mutations have been linked with cardiomyopathy; however, knowledge about mitochondrial tRNAs (mt-tRNAs) mutations in this disease remain inadequately understood. In fact, defects in mt-tRNA metabolism caused by pathogenic mutations may influence the functioning of the OXPHOS complexes, thereby

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McGuire, Andrew T., Robert A. B. Keates, Stephanie Cook, and Dev Mangroo. "Structural modeling identified the tRNA-binding domain of Utp8p, an essential nucleolar component of the nuclear tRNA export machinery of Saccharomyces cerevisiae." Biochemistry and Cell Biology 87, no. 2 (2009): 431–43. http://dx.doi.org/10.1139/o08-145.

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Utp8p is an essential 80 kDa intranuclear tRNA chaperone that transports tRNAs from the nucleolus to the nuclear tRNA export receptors in Saccharomyces cerevisiae . To help understand the mechanism of Utp8p function, predictive tools were used to derive a partial model of the tertiary structure of Utp8p. Secondary structure prediction, supported by circular dichroism measurements, indicated that Utp8p is divided into 2 domains: the N-terminal beta sheet and the C-terminal alpha helical domain. Tertiary structure prediction was more challenging, because the amino acid sequence of Utp8p is not d

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Saint-Léger, Adélaïde, Carla Bello, Pablo D. Dans, et al. "Saturation of recognition elements blocks evolution of new tRNA identities." Science Advances 2, no. 4 (2016): e1501860. http://dx.doi.org/10.1126/sciadv.1501860.

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Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that

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Bhatta, Arjun, Christian Dienemann, Patrick Cramer, and Hauke S. Hillen. "Structural basis of RNA processing by human mitochondrial RNase P." Nature Structural & Molecular Biology 28, no. 9 (2021): 713–23. http://dx.doi.org/10.1038/s41594-021-00637-y.

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AbstractHuman mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved

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Edwards, Ashley M., Maame A. Addo, and Patricia C. Dos Santos. "Extracurricular Functions of tRNA Modifications in Microorganisms." Genes 11, no. 8 (2020): 907. http://dx.doi.org/10.3390/genes11080907.

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Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular viability. Hence, the placement and prevalence of tRNA modifications affects the efficiency of aminoacyl tRNA synthetase (aaRS) reactions, interactions with the ribosome, and transient pairing with messenger RNA (mRNA). The synthesis and abundance

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Gagnon, Matthieu G., Jinzhong Lin, and Thomas A. Steitz. "Elongation factor 4 remodels the A-site tRNA on the ribosome." Proceedings of the National Academy of Sciences 113, no. 18 (2016): 4994–99. http://dx.doi.org/10.1073/pnas.1522932113.

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During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5′-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The struct

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Underwood, D. C., H. Knickerbocker, G. Gardner, D. P. Condliffe, and K. U. Sprague. "Silk gland-specific tRNA(Ala) genes are tightly clustered in the silkworm genome." Molecular and Cellular Biology 8, no. 12 (1988): 5504–12. http://dx.doi.org/10.1128/mcb.8.12.5504-5512.1988.

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To understand the basis for tissue-specific production and accumulation of alanine tRNA in silkworms, we have examined the organization of the genes that code for silk gland-specific and constitutive alanine tRNAs. We have found that all of the silk gland-specific tRNA(Ala) genes (approximately 20) appear to be tightly clustered at a single locus in the Bombyx genome. These genes are arranged in tandem at intervals of approximately 150 base pairs. In contrast to the arrangement of the silk gland-specific tRNA(Ala) genes, most of the 20 to 30 constitutive tRNA(Ala) genes are dispersed in the ge

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Underwood, D. C., H. Knickerbocker, G. Gardner, D. P. Condliffe, and K. U. Sprague. "Silk gland-specific tRNA(Ala) genes are tightly clustered in the silkworm genome." Molecular and Cellular Biology 8, no. 12 (1988): 5504–12. http://dx.doi.org/10.1128/mcb.8.12.5504.

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To understand the basis for tissue-specific production and accumulation of alanine tRNA in silkworms, we have examined the organization of the genes that code for silk gland-specific and constitutive alanine tRNAs. We have found that all of the silk gland-specific tRNA(Ala) genes (approximately 20) appear to be tightly clustered at a single locus in the Bombyx genome. These genes are arranged in tandem at intervals of approximately 150 base pairs. In contrast to the arrangement of the silk gland-specific tRNA(Ala) genes, most of the 20 to 30 constitutive tRNA(Ala) genes are dispersed in the ge

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Liu, Yuchen, David J. Vinyard, Megan E. Reesbeck, et al. "A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes." Proceedings of the National Academy of Sciences 113, no. 45 (2016): 12703–8. http://dx.doi.org/10.1073/pnas.1615732113.

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The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s4U) and 2-thiouridine (s2U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI fr

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Pinto, Paola H., Alena Kroupova, Alexander Schleiffer, et al. "ANGEL2 is a member of the CCR4 family of deadenylases with 2′,3′-cyclic phosphatase activity." Science 369, no. 6503 (2020): 524–30. http://dx.doi.org/10.1126/science.aba9763.

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RNA molecules are frequently modified with a terminal 2′,3′-cyclic phosphate group as a result of endonuclease cleavage, exonuclease trimming, or de novo synthesis. During pre-transfer RNA (tRNA) and unconventional messenger RNA (mRNA) splicing, 2′,3′-cyclic phosphates are substrates of the tRNA ligase complex, and their removal is critical for recycling of tRNAs upon ribosome stalling. We identified the predicted deadenylase angel homolog 2 (ANGEL2) as a human phosphatase that converts 2′,3′-cyclic phosphates into 2′,3′-OH nucleotides. We analyzed ANGEL2’s substrate preference, structure, and

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Strobel, M. C., and J. Abelson. "Intron mutations affect splicing of Saccharomyces cerevisiae SUP53 precursor tRNA." Molecular and Cellular Biology 6, no. 7 (1986): 2674–83. http://dx.doi.org/10.1128/mcb.6.7.2674-2683.1986.

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The Saccharomyces cerevisiae amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the role of intron structure and sequence on precursor tRNA splicing in vivo and in vitro. This gene encodes a pre-tRNA which contains a 32-base intervening sequence. Two types of SUP53 intron mutants were constructed: ones with an internal deletion of the natural SUP53 intron and ones with a novel intron. These mutant genes were transcribed in vitro, and the end-processed transcripts were analyzed for their ability to serve as substrates for the partially purified S. cerevisiae tRNA endon

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Strobel, M. C., and J. Abelson. "Intron mutations affect splicing of Saccharomyces cerevisiae SUP53 precursor tRNA." Molecular and Cellular Biology 6, no. 7 (1986): 2674–83. http://dx.doi.org/10.1128/mcb.6.7.2674.

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The Saccharomyces cerevisiae amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the role of intron structure and sequence on precursor tRNA splicing in vivo and in vitro. This gene encodes a pre-tRNA which contains a 32-base intervening sequence. Two types of SUP53 intron mutants were constructed: ones with an internal deletion of the natural SUP53 intron and ones with a novel intron. These mutant genes were transcribed in vitro, and the end-processed transcripts were analyzed for their ability to serve as substrates for the partially purified S. cerevisiae tRNA endon

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Antika, Titi Rindi, Dea Jolie Chrestella, Indira Rizqita Ivanesthi, et al. "Gain of C-Ala enables AlaRS to target the L-shaped tRNAAla." Nucleic Acids Research 50, no. 4 (2022): 2190–200. http://dx.doi.org/10.1093/nar/gkac026.

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Abstract Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRSc) retains the prototype structure, its mitochondrial counterpart (CeAlaRSm) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRSc robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNAAla. Deletion of this domain from CeAlaRSc sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRSm select

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Hong, Samuel, S. Sunita, Tatsuya Maehigashi, Eric D. Hoffer, Jack A. Dunkle, and Christine M. Dunham. "Mechanism of tRNA-mediated +1 ribosomal frameshifting." Proceedings of the National Academy of Sciences 115, no. 44 (2018): 11226–31. http://dx.doi.org/10.1073/pnas.1809319115.

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Accurate translation of the genetic code is critical to ensure expression of proteins with correct amino acid sequences. Certain tRNAs can cause a shift out of frame (i.e., frameshifting) due to imbalances in tRNA concentrations, lack of tRNA modifications or insertions or deletions in tRNAs (called frameshift suppressors). Here, we determined the structural basis for how frameshift-suppressor tRNASufA6 (a derivative of tRNAPro) reprograms the mRNA frame to translate a 4-nt codon when bound to the bacterial ribosome. After decoding at the aminoacyl (A) site, the crystal structure of the antico

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Shibata, Hirotaka S., Hiroaki Takaku, Masamichi Takagi, and Masayuki Nashimoto. "The T Loop Structure Is Dispensable for Substrate Recognition by tRNase ZL." Journal of Biological Chemistry 280, no. 23 (2005): 22326–34. http://dx.doi.org/10.1074/jbc.m502048200.

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tRNA 3′-processing endoribonucleases (tRNase Z, or 3′-tRNase; EC 3.1.26.11) are enzymes that remove 3′-trailers from pre-tRNAs. An about 12-base-pair stem, a T loop-like structure, and a 3′-trailer were considered to be the minimum requirements for recognition by the long form (tRNase ZL) of tRNase Z; tRNase ZL can recognize and cleave a micro-pre-tRNA or a hooker/target RNA complex that resembles a micro-pre-tRNA. We examined four hook RNAs containing systematically weakened T stems for directing target RNA cleavage by tRNase ZL. As expected, the cleavage efficiency decreased with the decreas

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Gupta, Yash Munnalal, Kittisak Buddhachat, Surin Peyachoknagul, and Somjit Homchan. "Collection of Mitochondrial tRNA Sequences and Anticodon Identification for Acheta domesticus." Materials Science Forum 967 (August 2019): 65–70. http://dx.doi.org/10.4028/www.scientific.net/msf.967.65.

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The mitochondria are organelles found within eukaryotic cell, possess own small circular DNA (mtDNA) apart from the most of DNA found in cell nucleus. The transcription and translation of mtDNA requires tRNA that often encoded by mtDNA itself. The mtDNA evolves faster than genomic DNA primary due to mitochondrial dysfunction and pathogenesis. The genes of mitochondria tRNA (mt tRNA) are prone to mutate that links to mitochondrial activity and protein synthesis machinery. It is important to understand the codon use by mt tRNA for Acheta domesticus to understand evolutionary relationship within

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Dörner, Marion, Markus Altmann, Svante Pääbo, and Mario Mörl. "Evidence for Import of a Lysyl-tRNA into Marsupial Mitochondria." Molecular Biology of the Cell 12, no. 9 (2001): 2688–98. http://dx.doi.org/10.1091/mbc.12.9.2688.

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The mitochondrial tRNA gene for lysine was analyzed in 11 different marsupial mammals. Whereas its location is conserved when compared with other vertebrate mitochondrial genomes, its primary sequence and inferred secondary structure are highly unusual and variable. For example, eight species lack the expected anticodon. Because the corresponding transcripts are not altered by any RNA-editing mechanism, the lysyl-tRNA gene seems to represent a mitochondrial pseudogene. Purification of marsupial mitochondria and in vitro aminoacylation of isolated tRNAs with lysine, followed by analysis of amin

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Kazuhito, Tomizawa, and Fan-Yan Wei. "Posttranscriptional modifications in mitochondrial tRNA and its implication in mitochondrial translation and disease." Journal of Biochemistry 168, no. 5 (2020): 435–44. http://dx.doi.org/10.1093/jb/mvaa098.

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Abstract A fundamental aspect of mitochondria is that they possess DNA and protein translation machinery. Mitochondrial DNA encodes 22 tRNAs that translate mitochondrial mRNAs to 13 polypeptides of respiratory complexes. Various chemical modifications have been identified in mitochondrial tRNAs via complex enzymatic processes. A growing body of evidence has demonstrated that these modifications are essential for translation by regulating tRNA stability, structure and mRNA binding, and can be dynamically regulated by the metabolic environment. Importantly, the hypomodification of mitochondrial

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Noller, Harry F., Rachel Green, Gabriele Heilek, et al. "Structure and function of ribosomal RNA." Biochemistry and Cell Biology 73, no. 11-12 (1995): 997–1009. http://dx.doi.org/10.1139/o95-107.

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A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe2+–EDTA complex. A second approach uses localized hydroxyl radical cleavage from a single Fe2+tethered to unique positions on the surface of single proteins in the 30S subunit. This has been carried out for one position on the surface of protein S4, two on S17, and three on S5. Nucleotides in 16S rRNA that are ess

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Mathison, L., M. Winey, C. Soref, M. R. Culbertson, and G. Knapp. "Mutations in the anticodon stem affect removal of introns from pre-tRNA in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 10 (1989): 4220–28. http://dx.doi.org/10.1128/mcb.9.10.4220-4228.1989.

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To evaluate the role of exon domains in tRNA splicing, the anti-codon stem of proline pre-tRNAUGG from Saccharomyces cerevisiae was altered by site-directed mutagenesis of the suf8 gene. Sixteen alleles were constructed that encode mutant pre-tRNAs containing all possible base combinations in the last base pair of the anticodon stem adjacent to the anticodon loop (positions 31 and 39). The altered pre-tRNAs were screened by using an in vitro endonucleolytic cleavage assay to determine whether perturbations in secondary structure affect the intron excision reaction. The pre-tRNAs were cleaved e

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Mathison, L., M. Winey, C. Soref, M. R. Culbertson, and G. Knapp. "Mutations in the anticodon stem affect removal of introns from pre-tRNA in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 10 (1989): 4220–28. http://dx.doi.org/10.1128/mcb.9.10.4220.

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To evaluate the role of exon domains in tRNA splicing, the anti-codon stem of proline pre-tRNAUGG from Saccharomyces cerevisiae was altered by site-directed mutagenesis of the suf8 gene. Sixteen alleles were constructed that encode mutant pre-tRNAs containing all possible base combinations in the last base pair of the anticodon stem adjacent to the anticodon loop (positions 31 and 39). The altered pre-tRNAs were screened by using an in vitro endonucleolytic cleavage assay to determine whether perturbations in secondary structure affect the intron excision reaction. The pre-tRNAs were cleaved e

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Agmon, Ilana. "Prebiotic Assembly of Cloverleaf tRNA, Its Aminoacylation and the Origin of Coding, Inferred from Acceptor Stem Coding-Triplets." International Journal of Molecular Sciences 23, no. 24 (2022): 15756. http://dx.doi.org/10.3390/ijms232415756.

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tRNA is a key component in life’s most fundamental process, the translation of the instructions contained in mRNA into proteins. Its role had to be executed as soon as the earliest translation emerged, but the questions of the prebiotic tRNA materialization, aminoacylation, and the origin of the coding triplets it carries are still open. Here, these questions are addressed by utilizing a distinct pattern of coding triplets highly conserved in the acceptor stems from the modern bacterial tRNAs of five early-emerging amino acids. Self-assembly of several copies of a short RNA oligonucleotide tha

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MANS, Ruud M. W., Cornelis W. A. PLEIJ, and Leendert BOSCH. "tRNA-like structures. Structure, function and evolutionary significance." European Journal of Biochemistry 201, no. 2 (1991): 303–24. http://dx.doi.org/10.1111/j.1432-1033.1991.tb16288.x.

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