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Journal articles on the topic 'TRNAfMet'

Author: Grafiati

Published: 6 September 2023

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1

Steiner-Mosonyi, Marta, Carole Creuzenet, Robert A. B. Keates, Benjamin R. Strub, and Dev Mangroo. "ThePseudomonas aeruginosaInitiation Factor IF-2 Is Responsible for Formylation-independent Protein Initiation inP. aeruginosa." Journal of Biological Chemistry 279, no. 50 (September 22, 2004): 52262–69. http://dx.doi.org/10.1074/jbc.m408086200.

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Formylation of the initiator methionyl-tRNA (Met-tRNAfMet) was generally thought to be essential for initiation of protein synthesis in all eubacteria based on studies conducted primarily inEscherichia coli. However, this view of eubacterial protein initiation has changed because some bacteria have been demonstrated to have the capacity to initiate protein synthesis with the unformylated Met-tRNAfMet. Here we show that thePseudomonas aeruginosainitiation factor IF-2 is required for formylation-independent protein initiation inP. aeruginosa, the first bacterium shown to have the ability to initiate protein synthesis with both the initiator formyl-methionyl-tRNA (fMet-tRNAfMet) and Met-tRNAfMet. TheE. coliIF-2, which participates exclusively in formylation-dependent protein initiation inE. coli, was unable to facilitate utilization of Met-tRNAfMetin initiation inP. aeruginosa. However, theE. coliIF-2 was made to function in formylation-independent protein initiation inP. aeruginosaby decreasing the positive charge potential of the cleft that binds the amino end of the amino acid attached to the tRNA. Furthermore increasing the positive charge potential of this cleft in theP. aeruginosaIF-2 prevented the protein from participating in formylation-independent protein initiation. Thus, this is the first demonstration of a eubacterial IF-2 with an inherent capacity to facilitate utilization of Met-tRNAfMetin protein initiation, discounting the dogma that eubacterial IF-2 can only allow the use of fMet-tRNAfMetin protein initiation. Furthermore these findings give important clues to the basis for discriminating the initiator Met-tRNA by IF-2 and for the evolution of alternative mechanisms for discrimination.

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2

Li, Yan, William B. Holmes, Dean R. Appling, and Uttam L. RajBhandary. "Initiation of Protein Synthesis in Saccharomyces cerevisiae Mitochondria without Formylation of the Initiator tRNA." Journal of Bacteriology 182, no. 10 (May 15, 2000): 2886–92. http://dx.doi.org/10.1128/jb.182.10.2886-2892.2000.

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ABSTRACT Protein synthesis in eukaryotic organelles such as mitochondria and chloroplasts is widely believed to require a formylated initiator methionyl tRNA (fMet-tRNAfMet) for initiation. Here we show that initiation of protein synthesis in yeast mitochondria can occur without formylation of the initiator methionyl-tRNA (Met-tRNAfMet). The formylation reaction is catalyzed by methionyl-tRNA formyltransferase (MTF) located in mitochondria and usesN 10-formyltetrahydrofolate (10-formyl-THF) as the formyl donor. We have studied yeast mutants carrying chromosomal disruptions of the genes encoding the mitochondrial C1-tetrahydrofolate (C1-THF) synthase (MIS1), necessary for synthesis of 10-formyl-THF, and the methionyl-tRNA formyltransferase (open reading frame YBL013W; designated FMT1). A direct analysis of mitochondrial tRNAs using gel electrophoresis systems that can separate fMet-tRNAfMet, Met-tRNAfMet, and tRNAfMet shows that there is no formylation in vivo of the mitochondrial initiator Met-tRNA in these strains. In contrast, the initiator Met-tRNA is formylated in the respective “wild-type” parental strains. In spite of the absence of fMet-tRNAfMet, the mutant strains exhibited normal mitochondrial protein synthesis and function, as evidenced by normal growth on nonfermentable carbon sources in rich media and normal frequencies of generation ofpetite colonies. The only growth phenotype observed was a longer lag time during growth on nonfermentable carbon sources in minimal media for the mis1 deletion strain but not for thefmt1 deletion strain.

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3

Fratte, Sonia Delle, Chiara Piubelli, and Enrico Domenici. "Development of a High-Throughput Scintillation Proximity Assay for the Identification of C-Domain Translational Initiation Factor 2 Inhibitors." Journal of Biomolecular Screening 7, no. 6 (December 2002): 541–46. http://dx.doi.org/10.1177/1087057102238628.

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Translational initiation factor 2 (IF2) is the largest of the 3 factors required for translation initiation in prokaryotes and has been shown to be essential in Escherichia coli. It stimulates the binding of fMet-tRNAfMet to the 30S ribosomal subunit in the presence of GTP. The selectivity is achieved through specific recognition of the tRNAfMet blocked α-amino group. IF2 is composed of 3 structural domains: N-domain, whose function is not known; G-domain, which contains the GTP/GDP binding site and the GTPase catalytic center; and C-domain, which recognizes and binds fMet-tRNAfMet. Its activity is strictly bacteria specific and highly conserved among prokaryotes. So far, antibiotics targeting IF2 function are not known, and this makes it an ideal target for new drugs with mechanisms of resistance not yet developed. A few assays have been developed in the past, which allow the detection of IF2 activity either directly or indirectly. In both instances, the assays are based on radioactive detection and do not allow for high throughput because of the need for separation or solvent extraction steps. The authors describe a novel biochemical assay for IF2 that exploits the molecular recognition of fMet-tRNAfMet by the C-domain. The assay is based on the incubation of biotinyl-IF2 with fMet-tRNAfMet and the subsequent capture of the radiolabeled complex by streptavidin-coated beads, exploiting the scintillation proximity assay (SPA) technology. The assay has been designed in an automatable, homogeneous, miniaturized fashion suitable for high-throughput screening and is rapid, sensitive, and robust to dimethyl sulfoxide (DMSO) up to 10% v/v. The assay, used to screen a limited chemical collection of about 5000 compounds and a subset of compounds originated by a 2-D substructural search, has shown to be able to detect potential IF2 inhibitors.

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4

Schmitt, Emmanuelle, Michel Panvert, Sylvain Blanquet, and Yves Mechulam. "Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet." EMBO Journal 17, no. 23 (December 1, 1998): 6819–26. http://dx.doi.org/10.1093/emboj/17.23.6819.

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5

Polishchuk, L. V. "Nucleotide sequences of tRNA-methonine genes of Streptomyces globisporus 1912-2, identified in silico." Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv 14, no. 1 (June 20, 2016): 58–62. http://dx.doi.org/10.7124/visnyk.utgis.14.1.545.

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Aim of this work was to identify nucleotide sequences of tRNAMet of S. globisporus 1912-2. Methods. Resources of server NCBI (programs BLAST: blast, discontiguous megablast and databases: “Genome”, “Nucleotide”) were used for in silico analysis of library of S. grlobisporus 1912-2 contigs. Results. Nucleotide sequences of 4 genes of tRNAMet of S. globisporus 1912-2 were determined in silico. Molecules of tRNA of the II type were translated from tRNAMet gene (Contig No 21 (936–1008 bp)) and the molecules of tRNAfMet genes (Contigs No 299 (1713–1787 bp), No 255 (5941–6015 bp)). Conclusions. 4 genes of transfer RNAs-methionine were identified in silico in S. globisporus 1912-2 genome. Two genes from them coded tRNAfMet molecules. The nucleotide sequences of all tRNAMet genes were identified.Keywords: gene, tRNA, methionine, nucleotide sequence, Streptomyces.

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6

Nomura, Teruaki, Nobuyuki Fujita, and Akira Ishihama. "Promoter selectivity ofEscherichia coliRNA polymerase: alteration by fMet-tRNAfMet." Nucleic Acids Research 14, no. 17 (1986): 6857–70. http://dx.doi.org/10.1093/nar/14.17.6857.

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7

Rodnina, M. V., Y. P. Semenkov, and W. Wintermeyer. "Purification of fMET-tRNAfMET by Fast Protein Liquid Chromatography." Analytical Biochemistry 219, no. 2 (June 1994): 380–81. http://dx.doi.org/10.1006/abio.1994.1282.

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8

Ferguson, Blair Q., and David C. H. Yang. "Topographic modeling of free and methionyl-tRNA synthetase-bound tRNAfMet by singlet-singlet energy transfer: bending of the 3'-terminal arm in tRNAfMet." Biochemistry 25, no. 21 (October 1986): 6572–78. http://dx.doi.org/10.1021/bi00369a035.

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9

Duroc, Yann, Carmela Giglione, and Thierry Meinnel. "Mutations in Three Distinct Loci Cause Resistance to Peptide Deformylase Inhibitors in Bacillus subtilis." Antimicrobial Agents and Chemotherapy 53, no. 4 (January 26, 2009): 1673–78. http://dx.doi.org/10.1128/aac.01340-08.

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ABSTRACT Bacillus subtilis mutants with resistance against peptide deformylase inhibitors were isolated. All showed a bypass of the pathway through mutations in three genes required for formylation of Met-tRNAfMet, fmt, folD, and glyA. glyA corresponds to a yet uncharacterized locus inducing resistance. The bypass of formylation caused robust fitness reduction but was not accompanied by alterations of the transcription profile. A subtle adaptation of the enzymes of the intermediary metabolism was observed.

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10

Guenneugues, Marc, Enrico Caserta, Letizia Brandi, Roberto Spurio, Sylvie Meunier, Cynthia L. Pon, Rolf Boelens, and Claudio O. Gualerzi. "Mapping the fMet-tRNAfMet binding site of initiation factor IF2." EMBO Journal 19, no. 19 (October 2, 2000): 5233–40. http://dx.doi.org/10.1093/emboj/19.19.5233.

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11

Donga, Robert A., Tak-Hang Chan, and Masad J. Damha. "Ion-tagged synthesis of an oligoribonucleotide pentamer — The continuing versatility of TBDMS chemistry." Canadian Journal of Chemistry 85, no. 4 (April 1, 2007): 274–82. http://dx.doi.org/10.1139/v07-022.

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An oligoribonucleotide has been synthesized in solution, using an ionic-liquid-based soluble tag at a scale several hundred times that of a standard solid-phase synthesis approach. Ogilvie's 2′-TBDMS strategy was adopted, and because of the resultant increase in lipophilicity, it allowed an easier purification of the growing oligomer compared with the previously observed for DNA, which does not require 2′ protection. The procedure is illustrated by the synthesis of the pentaribonucleotide sequence AGAUC, corresponding to a segment of the tRNAfMet from E. coli.Key words: solution-phase RNA synthesis, ionic-liquid tag.

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12

Jurėnas, Dukas, Sneha Chatterjee, Albert Konijnenberg, Frank Sobott, Louis Droogmans, Abel Garcia-Pino, and Laurence Van Melderen. "AtaT blocks translation initiation by N-acetylation of the initiator tRNAfMet." Nature Chemical Biology 13, no. 6 (April 3, 2017): 640–46. http://dx.doi.org/10.1038/nchembio.2346.

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13

Schmitt, Emmanuelle, Yves Mechulam, Marc Ruff, Andre Mitschler, Dino Moras, and Sylvain Blanquet. "Crystallization and preliminary X-ray analysis ofEscherichia coli methionyl–tRNAfMet formyltransferase." Proteins: Structure, Function, and Genetics 25, no. 1 (May 1996): 139–41. http://dx.doi.org/10.1002/prot.14.

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14

Meunier, S. "Structure of the fMet-tRNAfMet-binding domain of B.stearothermophilus initiation factor IF2." EMBO Journal 19, no. 8 (April 17, 2000): 1918–26. http://dx.doi.org/10.1093/emboj/19.8.1918.

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15

Guillon, Jean-Michel, Thierry Meinnel, Yves Mechulam, Christine Lazennec, Sylvain Blanquet, and Guy Fayat. "Nucleotides of tRNA governing the specificity of Escherichia coli methionyl-tRNAfMet formyltransferase." Journal of Molecular Biology 224, no. 2 (March 1992): 359–67. http://dx.doi.org/10.1016/0022-2836(92)91000-f.

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16

Schmitt, Emmanuelle, Yves Mechulam, Marc Ruff, Andre Mitschler, Dino Moras, and Sylvain Blanquet. "Crystallization and preliminary x‐ray analysis of Escherichia coli methionyl‐tRNAfMet formyltransferase." Proteins: Structure, Function, and Genetics 25, no. 1 (May 1996): 139–41. http://dx.doi.org/10.1002/(sici)1097-0134(199605)25:1<139::aid-prot14>3.3.co;2-z.

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17

Biedenbänder, Thomas, Vanessa de Jesus, Martina Schmidt-Dengler, Mark Helm, Björn Corzilius, and Boris Fürtig. "RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics." Nucleic Acids Research 50, no. 4 (February 7, 2022): 2334–49. http://dx.doi.org/10.1093/nar/gkac040.

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Abstract A plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA’s secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates.

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18

Roy, Bappaditya, Qi Liu, Shinichiro Shoji, and Kurt Fredrick. "IF2 and unique features of initiator tRNAfMet help establish the translational reading frame." RNA Biology 15, no. 4-5 (November 13, 2017): 604–13. http://dx.doi.org/10.1080/15476286.2017.1379636.

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19

Pande, Chandramohan, and Arnold Wishnia. "Characterization of the fluorescent bimane derivative of E. coli initiator transfer RNA (tRNAfMet)." Biochemical and Biophysical Research Communications 127, no. 1 (February 1985): 49–55. http://dx.doi.org/10.1016/s0006-291x(85)80124-8.

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20

Meinnel, Thierry, Yves Mechulam, Sylvain Blanquet, and Guy Fayat. "Binding of the anticodon domain of tRNAfMet to Escherichia coli methionyl-tRNA synthetase." Journal of Molecular Biology 220, no. 2 (July 1991): 205–8. http://dx.doi.org/10.1016/0022-2836(91)90003-o.

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21

Takahiro, Nagase, Ishii Shunsuke, and Imamoto Fumio. "Differential transcriptional control of the two tRNAfMet genes of Escherichia coli K-12." Gene 67, no. 1 (July 1988): 49–57. http://dx.doi.org/10.1016/0378-1119(88)90007-8.

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22

Di Pietro, E., J. Sirois, M. L. Tremblay, and R. E. MacKenzie. "Mitochondrial NAD-Dependent Methylenetetrahydrofolate Dehydrogenase-Methenyltetrahydrofolate Cyclohydrolase Is Essential for Embryonic Development." Molecular and Cellular Biology 22, no. 12 (June 15, 2002): 4158–66. http://dx.doi.org/10.1128/mcb.22.12.4158-4166.2002.

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ABSTRACT Folate-dependent enzymes are compartmentalized between the cytoplasm and mitochondria of eukaryotes. The role of mitochondrial folate-dependent metabolism and the extent of its contribution to cytoplasmic processes are areas of active investigation. NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase (NMDMC) catalyzes the interconversion of 5,10-methylenetetrahydrofolate and 10-formyltetrahydrofolate in mitochondria of mammalian cells, but its metabolic role is not yet clear. Its expression in embryonic tissues but not in most adult tissues as well as its stringent transcriptional regulation led us to postulate that it may play a role in embryonic development. To investigate the metabolic role of NMDMC, we used a knockout approach to delete the nmdmc gene in mice. Heterozygous mice appear healthy, but homozygous NMDMC knockout mice die in utero. At embryonic day 12.5 (E12.5), homozygous null embryos exhibit no obvious developmental defects but are smaller and pale and die soon thereafter. Mutant fetal livers contain fewer nucleated cells and lack the characteristic redness of wild-type or heterozygous livers. The frequencies of CFU-erythroid (CFU-E) and burst-forming unit-erythroid (BFU-E) from fetal livers of E12.5 null mutants were not reduced compared with those of wild-type or heterozygous embryos. It has been assumed that initiation of protein synthesis in mitochondria requires a formylated methionyl-tRNAfmet. One role postulated for NMDMC is to provide 10-formyltetrahydrofolate as a formyl group donor for the synthesis of this formylmethionyl-tRNAfmet. To determine if the loss of NMDMC impairs protein synthesis and thus could be a cause of embryonic lethality, mitochondrial translation products were examined in cells in culture. Mitochondrial protein synthesis was unaffected in NMDMC-null mutant cell lines compared with the wild type. These results show that NMDMC is not required to support initiation of protein synthesis in mitochondria in isolated cells but instead demonstrate an essential role for mitochondrial folate metabolism during embryonic development.

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23

Ferguson, Blair Q., and David C. H. Yang. "tRNAfMet-induced conformational transition at the intersubunit domain of fluorescent-labeled methionyl-tRNA synthetase." Biochemistry 25, no. 10 (May 1986): 2743–48. http://dx.doi.org/10.1021/bi00358a001.

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24

Agrawal, Rajendra K., Christian M. T. Spahn, Pawel Penczek, Robert A. Grassucci, Knud H. Nierhaus, and Joachim Frank. "Visualization of Trna Movements on the Escherichia coli 70s Ribosome during the Elongation Cycle." Journal of Cell Biology 150, no. 3 (August 7, 2000): 447–60. http://dx.doi.org/10.1083/jcb.150.3.447.

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Three-dimensional cryomaps have been reconstructed for tRNA–ribosome complexes in pre- and posttranslocational states at 17-Å resolution. The positions of tRNAs in the A and P sites in the pretranslocational complexes and in the P and E sites in the posttranslocational complexes have been determined. Of these, the P-site tRNA position is the same as seen earlier in the initiation-like fMet-tRNAfMet-ribosome complex, where it was visualized with high accuracy. Now, the positions of the A- and E-site tRNAs are determined with similar accuracy. The positions of the CCA end of the tRNAs at the A site are different before and after peptide bond formation. The relative positions of anticodons of P- and E-site tRNAs in the posttranslocational state are such that a codon–anticodon interaction at the E site appears feasible.

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25

Mayer, C. "Conformational change of Escherichia coli initiator methionyl-tRNAfMet upon binding to methionyl-tRNA formyl transferase." Nucleic Acids Research 30, no. 13 (July 1, 2002): 2844–50. http://dx.doi.org/10.1093/nar/gkf411.

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26

Bonocora, Richard P., and David A. Shub. "A novel group I intron-encoded endonuclease specific for the anticodon region of tRNAfMet genes." Molecular Microbiology 39, no. 5 (February 24, 2004): 1299–306. http://dx.doi.org/10.1111/j.1365-2958.2001.02318.x.

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27

Hansen, Peter Kamp, Brian F. C. Clark, and Hans Uffe Petersen. "Interaction between non-formylated initiator Met-tRNAfMet and the ribosomal A-site from Escherichia coli." Biochimie 69, no. 8 (August 1987): 871–77. http://dx.doi.org/10.1016/0300-9084(87)90214-8.

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28

Johansson, Magnus, Ka-Weng Ieong, Stefan Trobro, Peter Strazewski, Johan Åqvist, Michael Y. Pavlov, and Måns Ehrenberg. "pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA." Proceedings of the National Academy of Sciences 108, no. 1 (December 17, 2010): 79–84. http://dx.doi.org/10.1073/pnas.1012612107.

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We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNAfMet to the aa-tRNAs Phe-tRNAPhe, Ala-tRNAAla, Gly-tRNAGly, Pro-tRNAPro, Asn-tRNAAsn, and Ile-tRNAIle, selected to cover a large range of intrinsic pKa-values for the α-amino group of their amino acids. The peptidyl transfer rates were different at pH 7.5 and displayed different pH-dependence, quantified as the pH-value, , at which the rate was half maximal. The -values were downshifted relative to the intrinsic pKa-value of aa-tRNAs in bulk solution. Gly-tRNAGly had the smallest downshift, while Ile-tRNAIle and Ala-tRNAAla had the largest downshifts. These downshifts correlate strongly with molecular dynamics (MD) estimates of the downshifts in pKa-values of these aa-tRNAs upon A-site binding. Our data show the chemistry of peptide bond formation to be rate limiting for peptidyl transfer at pH 7.5 in the Gly and Pro cases and indicate rate limiting chemistry for all six aa-tRNAs.

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29

Gross, Martin, Mark S. Rubino, and Suzanne M. Hessefort. "The conversion of eIF-2·GDP to eIF-2·GTP by eIF-2B requires Met-tRNAfMet." Biochemical and Biophysical Research Communications 181, no. 3 (December 1991): 1500–1507. http://dx.doi.org/10.1016/0006-291x(91)92109-w.

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30

Chan, Ka-Kong, Perry Rosen, Anthony Specian, Jr., Herbert Weissbach, and Carlos Spears. "Synthesis and Activity of a Tetrahydrofolate Inhibitor of the Enzyme N10-Formyl-H4-folate-Met-tRNAfMet Transformylase." HETEROCYCLES 24, no. 11 (1986): 3079. http://dx.doi.org/10.3987/r-1986-11-3079.

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31

PERREAULT, Jean-Pierre, Richard T. PON, Mei-yan JIANG, Nassim USMAN, Jana PIKA, Kelvin K. OGILVIE, and Robert CEDERGREN. "The synthesis and functional evaluation of RNA and DNA polymers having the sequence of Escherichia coli tRNAfMet." European Journal of Biochemistry 186, no. 1-2 (December 1989): 87–93. http://dx.doi.org/10.1111/j.1432-1033.1989.tb15181.x.

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32

Pelka, Heike, and LaDonne H. Schulman. "Study of the interaction of Escherichia coli methionyl-tRNA synthetase with tRNAfMet using chemical and enzymic probes." Biochemistry 25, no. 15 (July 1986): 4450–56. http://dx.doi.org/10.1021/bi00363a042.

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33

Krafft, Christoph, Annette Diehl, Stefan Laettig, Joachim Behlke, Udo Heinemann, Cynthia L. Pon, Claudio O. Gualerzi, and Heinz Welfle. "Interaction of fMet-tRNAfMet with the C-terminal domain of translational initiation factor IF2 from Bacillus stearothermophilus." FEBS Letters 471, no. 2-3 (April 10, 2000): 128–32. http://dx.doi.org/10.1016/s0014-5793(00)01377-6.

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34

Wagner, T., C. Rundquist, M. Gross, and P. B. Sigler. "Structural features that underlie the use of bacterial Met-tRNAfMet primarily as an elongator in eukaryotic protein synthesis." Journal of Biological Chemistry 264, no. 31 (November 1989): 18506–11. http://dx.doi.org/10.1016/s0021-9258(18)51496-4.

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35

Ferguson, Blair Q., and David C. H. Yang. "Localization of noncovalently bound ethidium in free and methionyl-tRNA synthetase bound tRNAfMet by singlet-singlet energy transfer." Biochemistry 25, no. 18 (September 1986): 5298–304. http://dx.doi.org/10.1021/bi00366a046.

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36

Hountondji, Codjo, Sylvain Blanquet, and Florence Lederer. "Methionyl-tRNA synthetase from Escherichia coli: primary structure at the binding site for the 3'-end of tRNAfMet." Biochemistry 24, no. 5 (February 26, 1985): 1175–80. http://dx.doi.org/10.1021/bi00326a018.

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37

Stolboushkina, Elena, Stanislav Nikonov, Natalia Zelinskaya, Valentina Arkhipova, Alexei Nikulin, Maria Garber, and Oleg Nikonov. "Crystal Structure of the Archaeal Translation Initiation Factor 2 in Complex with a GTP Analogue and Met-tRNAfMet." Journal of Molecular Biology 425, no. 6 (March 2013): 989–98. http://dx.doi.org/10.1016/j.jmb.2012.12.023.

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38

Shu, H. H., C. A. Wise, G. D. Clark-Walker, and N. C. Martin. "A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA." Molecular and Cellular Biology 11, no. 3 (March 1991): 1662–67. http://dx.doi.org/10.1128/mcb.11.3.1662-1667.1991.

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We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.

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39

Krawczak, Felipe S., Marcelo B. Labruna, Joy A. Hecht, Christopher D. Paddock, and Sandor E. Karpathy. "Genotypic Characterization of Rickettsia bellii Reveals Distinct Lineages in the United States and South America." BioMed Research International 2018 (2018): 1–8. http://dx.doi.org/10.1155/2018/8505483.

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The bacterium Rickettsia bellii belongs to a basal group of rickettsiae that diverged prior to the pathogenic spotted fever group and typhus group Rickettsia species. Despite a diverse representation of R. bellii across more than 25 species of hard and soft ticks in the American continent, phylogeographical relationships among strains of this basal group-Rickettsia species are unknown; the work described here explores these relationships. DNA was extracted from 30 R. bellii tick isolates: 15 from the United States, 14 from Brazil, and 1 from Argentina. A total of 2,269 aligned nucleotide sites of 3 protein coding genes (gltA, atpA, and coxA) and 2 intergenic regions (rpmE-tRNAfmet and RC1027-xthA2) were concatenated and subjected to phylogenetic analysis by Bayesian methods. Results showed a separation of almost all isolates between North and South Americas, suggesting that they have radiated within their respective continents. Phylogenetic positions of the 30 isolates could be a result of not only their geographical origin but also the tick hosts they have coevolved with. Whether R. bellii originated with ticks in North or South America remains obscure, as our analyses did not show evidence for greater genetic divergence of R. bellii in either continent.

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40

Shu, H. H., C. A. Wise, G. D. Clark-Walker, and N. C. Martin. "A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA." Molecular and Cellular Biology 11, no. 3 (March 1991): 1662–67. http://dx.doi.org/10.1128/mcb.11.3.1662.

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We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.

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Battermann, Anja, Claudia Disse-Krömker, and Brigitte Dreiseikelmann. "A functional plasmid-borne rrn operon in soil isolates belonging to the genus Paracoccus." Microbiology 149, no. 12 (December 1, 2003): 3587–93. http://dx.doi.org/10.1099/mic.0.26608-0.

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Plasmid analysis of isolates from a small Paracoccus population revealed that all 15 representatives carried at least one endogenous plasmid of 23 or 15 kb in size, in addition to further plasmids of different sizes. It was shown by restriction analysis and hybridization that the 23 and 15 kb plasmids from the different isolates were identical or very similar to each other. By partial sequencing of pOL18/23, one of the 23 kb plasmids, a complete rrn operon with the structural genes for 16S, 23S and 5S rRNA, two genes for tRNAIle and tRNAAla within the spacer between the 16S and 23S rRNA genes, and a final tRNAfMet at the end of the operon were discovered. Expression of a green fluorescent protein gene (gfp) after insertion of a DNA fragment from the region upstream of the rRNA genes into a promoter-probe vector demonstrated that the rrn promoter region is functional. The rrn operon encoded by plasmid pOL18/23 is the first complete rrn operon sequenced from a strain of the genus Paracoccus, and only the second example of an rrn operon on a small plasmid.

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42

Davis, D. R., R. H. Griffey, Z. Yamaizumi, S. Nishimura, and C. D. Poulter. "15N-labeled tRNA. Identification of dihydrouridine in Escherichia coli tRNAfMet, tRNALys, and tRNAPhe by 1H-15N two-dimensional NMR." Journal of Biological Chemistry 261, no. 8 (March 1986): 3584–87. http://dx.doi.org/10.1016/s0021-9258(17)35686-7.

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Barraud, Pierre, Emmanuelle Schmitt, Yves Mechulam, Frédéric Dardel, and Carine Tisné. "A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis." Nucleic Acids Research 36, no. 15 (July 23, 2008): 4894–901. http://dx.doi.org/10.1093/nar/gkn462.

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Griffey, R. H., D. Davis, Z. Yamaizumi, S. Nishimura, A. Bax, B. Hawkins, and C. D. Poulter. "15N-labeled Escherichia coli tRNAfMet, tRNAGlu, tRNATyr, and tRNAPhe. Double resonance and two-dimensional NMR of N1-labeled pseudouridine." Journal of Biological Chemistry 260, no. 17 (August 1985): 9734–41. http://dx.doi.org/10.1016/s0021-9258(17)39300-6.

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45

Levin, Itay, Moshe Mevarech, and Bruce A. Palfey. "Characterization of a Novel Bifunctional Dihydropteroate Synthase/Dihydropteroate Reductase Enzyme from Helicobacter pylori." Journal of Bacteriology 189, no. 11 (April 6, 2007): 4062–69. http://dx.doi.org/10.1128/jb.01878-06.

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ABSTRACT Tetrahydrofolate is a ubiquitous C1 carrier in many biosynthetic pathways in bacteria, importantly, in the biosynthesis of formylmethionyl tRNAfMet, which is essential for the initiation of translation. The final step in the biosynthesis of tetrahydrofolate is carried out by the enzyme dihydrofolate reductase (DHFR). A search of the complete genome sequence of Helicobacter pylori failed to reveal any sequence that encodes DHFR. Previous studies demonstrated that the H. pylori dihydropteroate synthase gene folP can complement an Escherichia coli strain in which folA and folM, encoding two distinct DHFRs, are deleted. It was also shown that H. pylori FolP possesses an additional N-terminal domain that binds flavin mononucleotide (FMN). Homologous domains are found in FolP proteins of other microorganisms that do not possess DHFR. In this study, we demonstrated that H. pylori FolP is also a dihydropteroate reductase that derives its reducing power from soluble flavins, reduced FMN and reduced flavin adenine dinucleotide. We also determined the stoichiometry of the enzyme-bound flavin and showed that half of the bound flavin is exchangeable with the soluble flavins. Finally, site-directed mutagenesis of the most conserved amino acid residues in the N-terminal domain indicated the importance of these residues for the activity of the enzyme as a dihydropteroate reductase.

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46

Džupponová, Veronika, Nataša Tomášková, Andrea Antošová, Erik Sedlák, and Gabriel Žoldák. "Salt-Specific Suppression of the Cold Denaturation of Thermophilic Multidomain Initiation Factor 2." International Journal of Molecular Sciences 24, no. 7 (April 5, 2023): 6787. http://dx.doi.org/10.3390/ijms24076787.

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Thermophilic proteins and enzymes are attractive for use in industrial applications due to their resistance against heat and denaturants. Here, we report on a thermophilic protein that is stable at high temperatures (Ttrs, hot 67 °C) but undergoes significant unfolding at room temperature due to cold denaturation. Little is known about the cold denaturation of thermophilic proteins, although it can significantly limit their applications. We investigated the cold denaturation of thermophilic multidomain protein translation initiation factor 2 (IF2) from Thermus thermophilus. IF2 is a GTPase that binds to ribosomal subunits and initiator fMet-tRNAfMet during the initiation of protein biosynthesis. In the presence of 9 M urea, measurements in the far-UV region by circular dichroism were used to capture details about the secondary structure of full-length IF2 protein and its domains during cold and hot denaturation. Cold denaturation can be suppressed by salt, depending on the type, due to the decreased heat capacity. Thermodynamic analysis and mathematical modeling of the denaturation process showed that salts reduce the cooperativity of denaturation of the IF2 domains, which might be associated with the high frustration between domains. This characteristic of high interdomain frustration may be the key to satisfying numerous diverse contacts with ribosomal subunits, translation factors, and tRNA.

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Monestier, Auriane, Alexey Aleksandrov, Pierre-Damien Coureux, Michel Panvert, Yves Mechulam, and Emmanuelle Schmitt. "The structure of an E. coli tRNAfMet A1–U72 variant shows an unusual conformation of the A1–U72 base pair." RNA 23, no. 5 (January 31, 2017): 673–82. http://dx.doi.org/10.1261/rna.057877.116.

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48

Kenri, Tsuyoshi, Fumio Imamoto, and Yasunobu Kano. "Construction and characterization of an Escherichia coli mutant deficient in the metY gene encoding tRNAf2Met: either tRNAf1Met or tRNAf2Met is required for cell growth." Gene 114, no. 1 (May 1992): 109–14. http://dx.doi.org/10.1016/0378-1119(92)90715-2.

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Ferguson, Blair Q., and David C. H. Yang. "Methionyl-tRNA synthetase induced 3'-terminal and delocalized conformational transition in tRNAfMet: steady-state fluorescence of tRNA with a single fluorophore." Biochemistry 25, no. 3 (February 11, 1986): 529–39. http://dx.doi.org/10.1021/bi00351a002.

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Förster, Charlotte, Christoph Krafft, Heinz Welfle, Claudio O. Gualerzi, and Udo Heinemann. "Preliminary characterization by X-ray diffraction and Raman spectroscopy of a crystalline complex ofBacillus stearothermophilusinitiation factor 2 C-domain and fMet-tRNAfMet." Acta Crystallographica Section D Biological Crystallography 55, no. 3 (March 1, 1999): 712–16. http://dx.doi.org/10.1107/s0907444998014577.

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