Journal articles: 'TRNA Participation'

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Campos-Guillén, Juan, Jackeline Lizzeta Arvizu-Gómez, George H. Jones, and Gabriela Olmedo-Alvarez. "Characterization of tRNACys processing in a conditional Bacillus subtilis CCase mutant reveals the participation of RNase R in its quality control." Microbiology 156, no. 7 (July 1, 2010): 2102–11. http://dx.doi.org/10.1099/mic.0.034652-0.

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We generated a conditional CCase mutant of Bacillus subtilis to explore the participation in vivo of the tRNA nucleotidyltransferase (CCA transferase or CCase) in the maturation of the single-copy tRNACys, which lacks an encoded CCA 3′ end. We observed that shorter tRNACys species, presumably lacking CCA, only accumulated when the inducible Pspac : cca was introduced into an rnr mutant strain, but not in combination with pnp. We sequenced the tRNA 3′ ends produced in the various mutant tRNACys species to detect maturation and decay intermediates and observed that decay of the tRNACys occurs through the addition of poly(A) or heteropolymeric tails. A few clones corresponding to full-size tRNAs contained either CCA or other C and/or A sequences, suggesting that these are substrates for repair and/or decay. We also observed editing of tRNACys at position 21, which seems to occur preferentially in mature tRNAs. Altogether, our results provide in vivo evidence for the participation of the B. subtilis cca gene product in the maturation of tRNAs lacking CCA. We also suggest that RNase R exoRNase in B. subtilis participates in the quality control of tRNA.

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Weinger, Joshua S., and Scott A. Strobel. "Participation of the tRNA A76 Hydroxyl Groups throughout Translation†." Biochemistry 45, no. 19 (May 2006): 5939–48. http://dx.doi.org/10.1021/bi060183n.

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Shetty, Sunil, and Umesh Varshney. "An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation." Proceedings of the National Academy of Sciences 113, no. 41 (October 3, 2016): E6126—E6134. http://dx.doi.org/10.1073/pnas.1609550113.

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Ribosome biogenesis, a complex multistep process, results in correct folding of rRNAs, incorporation of >50 ribosomal proteins, and their maturation. Deficiencies in ribosome biogenesis may result in varied faults in translation of mRNAs causing cellular toxicities and ribosomopathies in higher organisms. How cells ensure quality control in ribosome biogenesis for the fidelity of its complex function remains unclear. Using Escherichia coli, we show that initiator tRNA (i-tRNA), specifically the evolutionarily conserved three consecutive GC base pairs in its anticodon stem, play a crucial role in ribosome maturation. Deficiencies in cellular contents of i-tRNA confer cold sensitivity and result in accumulation of ribosomes with immature 3′ and 5′ ends of the 16S rRNA. Overexpression of i-tRNA in various strains rescues biogenesis defects. Participation of i-tRNA in the first round of initiation complex formation licenses the final steps of ribosome maturation by signaling RNases to trim the terminal extensions of immature 16S rRNA.

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Ovchinnikov, Stepan V., Dmitry Bikmetov, Alexei Livenskyi, Marina Serebryakova, Brendan Wilcox, Kyle Mangano, Dmitrii I. Shiriaev, et al. "Mechanism of translation inhibition by type II GNAT toxin AtaT2." Nucleic Acids Research 48, no. 15 (June 29, 2020): 8617–25. http://dx.doi.org/10.1093/nar/gkaa551.

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Abstract Type II toxin–antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin–antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin–antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not evoke a stringent response. In vitro, AtaT2 acetylates the aminoacyl moiety of isoaccepting glycyl tRNAs, thus precluding their participation in translation. Our study broadens the known target specificity of GNAT toxins beyond the earlier described isoleucine and formyl methionine tRNAs, and suggest that various GNAT toxins may have evolved to specificaly target other if not all individual aminoacyl tRNAs.

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Florencio-Martínez, Luis E., Andrés Cano-Santiago, Fabiola Mondragón-Rosas, Maricarmen Gómez-García, Carlos Flores-Pérez, Fiordaliso C. Román-Carraro, Luis A. Barocio-Rodríguez, Rebeca G. Manning-Cela, Tomás Nepomuceno-Mejía, and Santiago Martínez-Calvillo. "Participation of TFIIIB Subunit Brf1 in Transcription Regulation in the Human Pathogen Leishmania major." Genes 12, no. 2 (February 16, 2021): 280. http://dx.doi.org/10.3390/genes12020280.

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In yeast and higher eukaryotes, transcription factor TFIIIB is required for accurate initiation of transcription by RNA Polymerase III (Pol III), which synthesizes transfer RNAs (tRNAs), 5S ribosomal RNA (rRNA), and other essential RNA molecules. TFIIIB is composed of three subunits: B double prime 1 (Bdp1), TATA-binding protein (TBP), and TFIIB-related factor 1 (Brf1). Here, we report the molecular characterization of Brf1 in Leishmania major (LmBrf1), a parasitic protozoan that shows distinctive transcription characteristics, including the apparent absence of Pol III general transcription factors TFIIIA and TFIIIC. Although single-knockout parasites of LmBrf1 were obtained, attempts to generate LmBrf1-null mutants were unsuccessful, which suggests that LmBrf1 is essential in promastigotes of L. major. Notably, Northern blot analyses showed that the half-lives of the messenger RNAs (mRNAs) from LmBrf1 and other components of the Pol III transcription machinery (Bdp1 and Pol III subunit RPC1) are very similar (~40 min). Stabilization of these transcripts was observed in stationary-phase parasites. Chromatin immunoprecipitation (ChIP) experiments showed that LmBrf1 binds to tRNA, small nuclear RNA (snRNA), and 5S rRNA genes. Unexpectedly, the results also indicated that LmBrf1 associates to the promoter region of the 18S rRNA genes and to three Pol II-dependent regions here analyzed. Tandem affinity purification and mass spectrometry analyses allowed the identification of a putative TFIIIC subunit. Moreover, several proteins involved in transcription by all three RNA polymerases co-purified with the tagged version of LmBrf1.

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Ossareh-Nazari, Batool, Christèle Maison, Ben E. Black, Lyne Lévesque, Bryce M. Paschal, and Catherine Dargemont. "RanGTP-Binding Protein NXT1 Facilitates Nuclear Export of Different Classes of RNA In Vitro." Molecular and Cellular Biology 20, no. 13 (July 1, 2000): 4562–71. http://dx.doi.org/10.1128/mcb.20.13.4562-4571.2000.

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ABSTRACT To better characterize the mechanisms responsible for RNA export from the nucleus, we developed an in vitro assay based on the use of permeabilized HeLa cells. This new assay supports nuclear export of U1 snRNA, tRNA, and mRNA in an energy- and Xenopusextract-dependent manner. U1 snRNA export requires a 5′ monomethylated cap structure, the nuclear export signal receptor CRM1, and the small GTPase Ran. In contrast, mRNA export does not require the participation of CRM1. We show here that NXT1, an NTF2-related protein that binds directly to RanGTP, strongly stimulates export of U1 snRNA, tRNA, and mRNA. The ability of NXT1 to promote export is dependent on its capacity to bind RanGTP. These results support the emerging view that NXT1 is a general export factor, functioning on both CRM1-dependent and CRM1-independent pathways of RNA export.

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Baldi, M., E. Mattoccia, E. Bufardeci, S. Fabbri, and G. Tocchini-Valentini. "Participation of the intron in the reaction catalyzed by the Xenopus tRNA splicing endonuclease." Science 255, no. 5050 (March 13, 1992): 1404–8. http://dx.doi.org/10.1126/science.1542788.

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MIZUTANI, TAKAHARU, KEIKO KANBE, YUKIKO KIMURA, YOSHIO TACHIBANA, and TERUAKI HITAKA. "Non-participation of opal suppressor phosphoseryl-transfer ribonucleic acid(tRNA) in phosphoserine aminotransferase catalysis." CHEMICAL & PHARMACEUTICAL BULLETIN 36, no. 2 (1988): 824–27. http://dx.doi.org/10.1248/cpb.36.824.

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9

Wada, M., K. Sekine, and H. Itikawa. "Participation of the dnaK and dnaJ gene products in phosphorylation of glutaminyl-tRNA synthetase and threonyl-tRNA synthetase of Escherichia coli K-12." Journal of Bacteriology 168, no. 1 (1986): 213–20. http://dx.doi.org/10.1128/jb.168.1.213-220.1986.

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10

Gawlik, Joanna, Michal Koper, Albert Bogdanowicz, Piotr Weglenski, and Agnieszka Dzikowska. "Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in Aspergillus nidulans." International Journal of Molecular Sciences 23, no. 19 (September 22, 2022): 11138. http://dx.doi.org/10.3390/ijms231911138.

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Kae1 is a subunit of the highly evolutionarily conserved KEOPS/EKC complex, which is involved in universal (t6A37) tRNA modification. Several reports have discussed the participation of this complex in transcription regulation in yeast and human cells, including our previous observations of KaeA, an Aspergillus nidulans homologue of Kae1p. The aim of this project was to confirm the role of KaeA in transcription, employing high-throughput transcriptomic (RNA-Seq and ChIP-Seq) and proteomic (LC-MS) analysis. We confirmed that KaeA is a subunit of the KEOPS complex in A. nidulans. An analysis of kaeA19 and kaeA25 mutants showed that, although the (t6A37) tRNA modification is unaffected in both mutants, they reveal significantly altered transcriptomes compared to the wild type. The finding that KaeA is localized in chromatin and identifying its protein partners allows us to postulate an additional nuclear function for the protein. Our data shed light on the universal bi-functional role of this factor and proves that the activity of this protein is not limited to tRNA modification in cytoplasm, but also affects the transcriptional activity of a number of nuclear genes. Data are available via the NCBI’s GEO database under identifiers GSE206830 (RNA-Seq) and GSE206874 (ChIP-Seq), and via ProteomeXchange with identifier PXD034554 (proteomic).

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Stiborová, Marie, and Pavel Anzenbacher. "Carcinogenic Non-Aminoazo Dye 1-Phenylazo-2-hydroxynaphthalene (Sudan I) Is Oxidized by Rat Liver Microsomal Cytochrome P-450 to Metabolites Binding to Macromolecules (Nucleic Acids and Proteins)." Collection of Czechoslovak Chemical Communications 57, no. 7 (1992): 1537–46. http://dx.doi.org/10.1135/cccc19921537.

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Carcinogenic non-aminoazo dye 1-phenylazo-2-hydroxynaphthalene (Sudan I) is oxidized by microsomal cytochromes P-450 to reactive metabolite(s) binding to macromolecules (nucleic acids, proteins) in vitro. The extent of binding to macromolecules proceeded in the order: protein > rRNA > tRNA > DNA. The patern of products formed from Sudan I and binding of the reactive metabolites of this compound to macromolecules are dependent on the concentration of Sudan I, NADPH and on the duration of the incubation. The participation of the adducts formed with macromolecules in the initiation of chemical carcinogenesis is discussed.

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Oh, Bong-Kyeong, Daniel N. Frank, and Norman R. Pace. "Participation of the 3‘-CCA of tRNA in the Binding of Catalytic Mg2+Ions by Ribonuclease P†." Biochemistry 37, no. 20 (May 1998): 7277–83. http://dx.doi.org/10.1021/bi973100z.

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13

Camiolo, Salvatore, Gaurav Sablok, and Andrea Porceddu. "The Evolutionary Basis of Translational Accuracy in Plants." G3 Genes|Genomes|Genetics 7, no. 7 (July 1, 2017): 2363–73. http://dx.doi.org/10.1534/g3.117.040626.

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Abstract Mistranslation errors compromise fitness by wasting resources on nonfunctional proteins. In order to reduce the cost of mistranslations, natural selection chooses the most accurately translated codons at sites that are particularly important for protein structure and function. We investigated the determinants underlying selection for translational accuracy in several species of plants belonging to three clades: Brassicaceae, Fabidae, and Poaceae. Although signatures of translational selection were found in genes from a wide range of species, the underlying factors varied in nature and intensity. Indeed, the degree of synonymous codon bias at evolutionarily conserved sites varied among plant clades while remaining uniform within each clade. This is unlikely to solely reflect the diversity of tRNA pools because there is little correlation between synonymous codon bias and tRNA abundance, so other factors must affect codon choice and translational accuracy in plant genes. Accordingly, synonymous codon choice at a given site was affected not only by the selection pressure at that site, but also its participation in protein domains or mRNA secondary structures. Although these effects were detected in all the species we analyzed, their impact on translation accuracy was distinct in evolutionarily distant plant clades. The domain effect was found to enhance translational accuracy in dicot and monocot genes with a high GC content, but to oppose the selection of more accurate codons in monocot genes with a low GC content.

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Lacourciere, Gerard M. "Selenium Is Mobilized In Vivo from Free Selenocysteine and Is Incorporated Specifically into Formate Dehydrogenase H and tRNA Nucleosides." Journal of Bacteriology 184, no. 7 (April 1, 2002): 1940–46. http://dx.doi.org/10.1128/jb.184.7.1940-1946.2002.

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ABSTRACT Selenophosphate synthetase (SPS), the selD gene product from Escherichia coli, catalyzes the biosynthesis of monoselenophosphate, AMP, and orthophosphate in a 1:1:1 ratio from selenide and ATP. It was recently demonstrated that selenium delivered from selenocysteine by an E. coli NifS-like protein could replace free selenide in the in vitro SPS assay for selenophosphate formation (G. M. Lacourciere, H. Mihara, T. Kurihara, N. Esaki, and T. C. Stadtman, J. Biol. Chem. 275:23769-23773, 2000). During growth of E. coli in the presence of 0.1 μM 75SeO3 2− and increasing amounts of l-selenocysteine, a concomitant decrease in 75Se incorporation into formate dehydrogenase H and nucleosides of bulk tRNA was observed. This is consistent with the mobilization of selenium from l-selenocysteine in vivo and its use in selenophosphate formation. The ability of E. coli to utilize selenocysteine as a selenium source for selenophosphate biosynthesis in vivo supports the participation of the NifS-like proteins in selenium metabolism.

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Shah, Riyaz Ahmad, Rajagopal Varada, Shivjee Sah, Sunil Shetty, Kuldeep Lahry, Sudhir Singh, and Umesh Varshney. "Rapid formylation of the cellular initiator tRNA population makes a crucial contribution to its exclusive participation at the step of initiation." Nucleic Acids Research 47, no. 4 (January 4, 2019): 1908–19. http://dx.doi.org/10.1093/nar/gky1310.

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Metjian, Ara, Yvette Tanhehco, Huy Phu Pham, Nicole A. Aqui, Vijay Bhoj, Oluwatoyosi Onwuemene, Marisa Marques, and Gowthami M. Arepally. "The Thrombotic Microangiopathy Registry of North America." Blood 126, no. 23 (December 3, 2015): 5587. http://dx.doi.org/10.1182/blood.v126.23.5587.5587.

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Abstract The thrombotic microangiopathies (TMAs) are rare, life-threatening thrombotic disorders of diverse etiologies. Systematic studies of TMA have been difficult to perform due to their rare occurrence, disease heterogeneity and, lack of an organized research network in the United States. Whereas a multi-institutional approach has been used in Europe and Canada, TMA research in the US has been largely single-center based. To overcome the limitations of single institutional registries and to expand the number of TMA patients available for study, four academic centers convened during the 2013 ASFA annual meeting to establish the TMA Registry of North America (TRNA) with the following goals: (1) design and develop a registry to define "best practices" for the diagnosis, treatment, and management of TMA; (2) develop a platform for conducting observational and interventional clinical trials; (3) and, establish a national bio-repository of samples from patients with TMA to facilitate future studies. This abstract reports the first multi-institutional network in the United States designed to study TMA. Members met through bimonthly tele-conferences to develop a clinical registry using REDCap (Research Electronic Data Capture), a HIPAA-compliant, internet-based software program for data entry. To facilitate a cohesive and streamlined review of IRB applications, the TRNA utilized IRBshare, a portal for rapid approval of multi-site investigations. IRB consent included participation in a bio-repository arm for collecting blood and apheresate. Following approval through the Duke IRB in June 2014, study documents were uploaded to the IRBshare website. Since August 2015, 16 study participants with TMA have been consented, 13 of which have had their clinical information entered into the database. Preliminary data shows our population is 73% African-American and female. Average laboratory values at presentation included hemoglobin of 9.7 g/dL, platelets 53 x10^9/L, and LDH 1,150 u/L. ADAMTS13 testing was performed in 77% (10/13), of which 60% (6/10) measured at <10%. Current efforts include expansion of network sites to expand the registry and to develop clinical protocols for future studies. With its clinical and IRB infrastructure in place, the TRNA, which is the first U.S. research network designed to study TMA, is poised to perform cooperative observational and interventional trials in the near future. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

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Denman, Robert, John Colgan, Kelvin Nurse, and James Ofengand. "Crosslinking of the anticodon of P site bound tRNA to C-1400 ofE.coli16S RNA does not require the participation of the 50S subunit." Nucleic Acids Research 16, no. 1 (1988): 165–78. http://dx.doi.org/10.1093/nar/16.1.165.

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Kazlovskiy, I. S., and M. A. Zinchenko. "Construction of a strain-producer of the chimeric protein consisting of RNA polymerase and a DNA-affinity domain." Doklady of the National Academy of Sciences of Belarus 62, no. 5 (October 30, 2018): 601–7. http://dx.doi.org/10.29235/1561-8323-2018-62-5-601-607.

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One of the recent perspective trends of molecular biotechnology is cell-free synthesis of protein. The procedure of cell-free synthesis of protein is based on in vitro reconstruction of all stages of a biosynthesis of protein in a whole cell, including a transcription, an aminoacylation of tRNA and translation of mRNA by ribosomes. Procreation of the transcription stage requires participation of specific RNA polymerase which initiates process of mRNA synthesis from the particular sites of recognition. Often the DNA-dependent RNA polymerase of a bacteriophage of T7 (T7 RNA polymerase) is for this purpose applied. For improvement of qualitative characteristics of the T7 RNA polymerase in the real work the new strain of Escherichia coli producing this enzyme fused with the DNA-affine Sso7d domain of a thermophilic bacterium Sulfolobus solfataricus is created. The producing ability of the received recombinant strain concerning synthesized chimera protein reaches 625 un/l of cultural liquid, and the specific activity of the purified enzyme preparation was 80 un/ μg of protein. The received enzyme is intended for use as tools at synthesis of proteins in cell-free system.

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Brown, Eric D. "Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology." Biochemistry and Cell Biology 83, no. 6 (December 1, 2005): 738–46. http://dx.doi.org/10.1139/o05-162.

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Establishing the roles of conserved gene products in bacteria is of fundamental importance to our understanding of the core protein complement necessary to sustain cellular life. P-loop GTPases and related ATPases represent an abundant and remarkable group of proteins in bacteria that, in many cases, have evaded characterization. Here, efforts aimed at understanding the cellular function of a group of 8 conserved, poorly characterized genes encoding P-loop GTPases, era, obg, trmE, yjeQ, engA, yihA, hflX, ychF, and a related ATPase, yjeE, are reviewed in considerable detail. While concrete cellular roles remain elusive for all of these genes and considerable pleiotropy has plagued their study, experiments to date have frequently implicated the ribosome. In the case of era, obg, yjeQ, and engA, the evidence is most consistent with roles in ribosome biogenesis, though the prediction is necessarily putative. While the protein encoded in trmE clearly has a catalytic function in tRNA modification, the participation of its GTPase domain remains obscure, as do the functions of the remaining proteins. A full understanding of the cellular functions of all of these important proteins remains the goal of ongoing studies of cellular phenotype and protein biochemistry.Key words: GTPase, unknown function, essential gene, P-loop.

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Basu, Arnab, Kathryn E. Shields, and Mee-Ngan F. Yap. "The hibernating 100S complex is a target of ribosome-recycling factor and elongation factor G in Staphylococcus aureus." Journal of Biological Chemistry 295, no. 18 (March 24, 2020): 6053–63. http://dx.doi.org/10.1074/jbc.ra119.012307.

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The formation of translationally inactive 70S dimers (called 100S ribosomes) by hibernation-promoting factor is a widespread survival strategy among bacteria. Ribosome dimerization is thought to be reversible, with the dissociation of the 100S complexes enabling ribosome recycling for participation in new rounds of translation. The precise pathway of 100S ribosome recycling has been unclear. We previously found that the heat-shock GTPase HflX in the human pathogen Staphylococcus aureus is a minor disassembly factor. Cells lacking hflX do not accumulate 100S ribosomes unless they are subjected to heat exposure, suggesting the existence of an alternative pathway during nonstressed conditions. Here, we provide biochemical and genetic evidence that two essential translation factors, ribosome-recycling factor (RRF) and GTPase elongation factor G (EF-G), synergistically split 100S ribosomes in a GTP-dependent but tRNA translocation-independent manner. We found that although HflX and the RRF/EF-G pair are functionally interchangeable, HflX is expressed at low levels and is dispensable under normal growth conditions. The bacterial RRF/EF-G pair was previously known to target only the post-termination 70S complexes; our results reveal a new role in the reversal of ribosome hibernation that is intimately linked to bacterial pathogenesis, persister formation, stress responses, and ribosome integrity.

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Noon, Kathleen R., Eveline Bruenger, and James A. McCloskey. "Posttranscriptional Modifications in 16S and 23S rRNAs of the Archaeal Hyperthermophile Sulfolobus solfataricus." Journal of Bacteriology 180, no. 11 (June 1, 1998): 2883–88. http://dx.doi.org/10.1128/jb.180.11.2883-2888.1998.

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ABSTRACT Posttranscriptional modification is common to many types of RNA, but the majority of information concerning structure and function of modification is derived principally from tRNA. By contrast, less is known about modification in rRNA in spite of accumulating evidence for its direct participation in translation. The structural identities and approximate molar levels of modifications have been established for 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfactaricus by using combined chromatography-mass spectrometry-based methods. Modification levels are exceptionally high for prokaryotic organisms, with approximately 38 modified sites in 16S rRNA and 50 in 23S rRNA for cells cultured at 75°C, compared with 11 and 23 sites, respectively, in Escherichia coli. We structurally characterized 10 different modified nucleosides in 16S rRNA, 64% (24 residues) of which are methylated at O-2′ of ribose, and 8 modified species in 23S rRNA, 86% (43 residues) of which are ribose methylated, a form of modification shown in earlier studies to enhance stability of the polynucleotide chain. From cultures grown at progressively higher temperatures, 60, 75, and 83°C, a slight trend toward increased ribose methylation levels was observed, with greatest net changes over the 23°C range shown for 2′-O-methyladenosine in 16S rRNA (21% increase) and for 2′-O-methylcytidine (24%) and 2′-O-methylguanosine (22%) in 23S rRNA. These findings are discussed in terms of the potential role of modification in stabilization of rRNA in the thermal environment.

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Ross-Inta, Catherine, Chern-Yi Tsai, and Cecilia Giulivi. "The mitochondrial pool of free amino acids reflects the composition of mitochondrial DNA-encoded proteins: indication of a post- translational quality control for protein synthesis." Bioscience Reports 28, no. 5 (September 11, 2008): 239–49. http://dx.doi.org/10.1042/bsr20080090.

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Mitochondria can synthesize a limited number of proteins encoded by mtDNA (mitochondrial DNA) by using their own biosynthetic machinery, whereas most of the proteins in mitochondria are imported from the cytosol. It could be hypothesized that the mitochondrial pool of amino acids follows the frequency of amino acids in mtDNA-encoded proteins or, alternatively, that the profile is the result of the participation of amino acids in pathways other than protein synthesis (e.g. haem biosynthesis and aminotransferase reactions). These hypotheses were tested by evaluating the pool of free amino acids and derivatives in highly-coupled purified liver mitochondria obtained from rats fed on a nutritionally adequate diet for growth. Our results indicated that the pool mainly reflects the amino acid composition of mtDNA-encoded proteins, suggesting that there is a post-translational control of protein synthesis. This conclusion was supported by the following findings: (i) correlation between the concentration of free amino acids in the matrix and the frequency of abundance of amino acids in mtDNA-encoded proteins; (ii) the similar ratios of essential-to-non-essential amino acids in mtDNA-encoded proteins and the mitochondrial pool of amino acids; and (iii), lack of a correlation between codon usage or tRNA levels and amino-acid concentrations. Quantitative information on the mammalian mitochondrial content of amino acids, such as that presented in the present study, along with functional studies, will help us to better understand the pathogenesis of mitochondrial diseases or the biochemical implications in mitochondrial metabolism.

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Lombard, Murielle, Colbie J. Reed, Ludovic Pecqueur, Bruno Faivre, Sabrine Toubdji, Claudia Sudol, Damien Brégeon, Valérie de Crécy-Lagard, and Djemel Hamdane. "Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family." Biomolecules 12, no. 12 (November 26, 2022): 1760. http://dx.doi.org/10.3390/biom12121760.

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Dihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus). So far, only bacterial Dus enzymes and their complexes with tRNAs have been structurally characterized. Understanding the structure-function relationships of eukaryotic Dus proteins has been hampered by the paucity of structural data. Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. Dus2 is the eukaryotic enzyme responsible for the synthesis of D20 in tRNAs and is involved in some human cancers and in the detoxification of β-amyloid peptides in Alzheimer’s disease. In addition to the domains forming the canonical structure of all Dus, i.e., the catalytic TIM-barrel domain and the helical domain, both participating in RNA recognition in the bacterial Dus, a majority of Dus2 proteins harbor extensions at both ends. While these are mainly unstructured extensions on the N-terminal side, the C-terminal side extensions can adopt well-defined structures such as helices and beta-sheets or even form additional domains such as zinc finger domains. 3D models of Dus2/tRNA complexes were also generated. This study suggests that eukaryotic Dus2 proteins may have an advantage in tRNA recognition over their bacterial counterparts due to their modularity.

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Yakobov, Nathaniel, Frédéric Fischer, Nassira Mahmoudi, Yusuke Saga, Christopher D. Grube, Hervé Roy, Bruno Senger, et al. "RNA-dependent sterol aspartylation in fungi." Proceedings of the National Academy of Sciences 117, no. 26 (June 15, 2020): 14948–57. http://dx.doi.org/10.1073/pnas.2003266117.

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Diverting aminoacyl-transfer RNAs (tRNAs) from protein synthesis is a well-known process used by a wide range of bacteria to aminoacylate membrane constituents. By tRNA-dependently adding amino acids to glycerolipids, bacteria change their cell surface properties, which intensifies antimicrobial drug resistance, pathogenicity, and virulence. No equivalent aminoacylated lipids have been uncovered in any eukaryotic species thus far, suggesting that tRNA-dependent lipid remodeling is a process restricted to prokaryotes. We report here the discovery of ergosteryl-3β-O-l-aspartate (Erg-Asp), a conjugated sterol that is produced by the tRNA-dependent addition of aspartate to the 3β-OH group of ergosterol, the major sterol found in fungal membranes. In fact, Erg-Asp exists in the majority of “higher” fungi, including species of biotechnological interest, and, more importantly, in human pathogens likeAspergillus fumigatus. We show that a bifunctional enzyme, ergosteryl-3β-O-l-aspartate synthase (ErdS), is responsible for Erg-Asp synthesis. ErdS corresponds to a unique fusion of an aspartyl-tRNA synthetase—that produces aspartyl-tRNAAsp(Asp-tRNAAsp)—and of aDomain of Unknown Function 2156, which actually transfers aspartate from Asp-tRNAAsponto ergosterol. We also uncovered that removal of the Asp modifier from Erg-Asp is catalyzed by a second enzyme, ErdH, that is a genuine Erg-Asp hydrolase participating in the turnover of the conjugated sterol in vivo. Phylogenomics highlights that the entire Erg-Asp synthesis/degradation pathway is conserved across “higher” fungi. Given the central roles of sterols and conjugated sterols in fungi, we propose that this tRNA-dependent ergosterol modification and homeostasis system might have broader implications in membrane remodeling, trafficking, antimicrobial resistance, or pathogenicity.

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Lipman, Alan. "Community Participation -- Hope and Reality." Transformation: Critical Perspectives on Southern Africa 53, no. 1 (2004): 53–68. http://dx.doi.org/10.1353/trn.2004.0009.

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Yang, Shiquan, Gaoyi Qu, Bixia Fu, Feng Yang, Weixian Zeng, Yunzhang Cai, Tao Ye, et al. "The function of KptA/Tpt1 gene – a minor review." Functional Plant Biology 47, no. 7 (2020): 577. http://dx.doi.org/10.1071/fp19159.

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Rapid response of uni- and multicellular organisms to environmental changes and their own growth is achieved through a series of molecular mechanisms, often involving modification of macromolecules, including nucleic acids, proteins and lipids. The ADP-ribosylation process has ability to modify these different macromolecules in cells, and is closely related to the biological processes, such as DNA replication, transcription, signal transduction, cell division, stress, microbial aging and pathogenesis. In addition, tRNA plays an essential role in the regulation of gene expression, as effector molecules, no-load tRNA affects the overall gene expression level of cells under some nutritional stress. KptA/Tpt1 is an essential phosphotransferase in the process of pre-tRNA splicing, releasing mature tRNA and participating in ADP-ribose. The objective of this review is concluding the gene structure, the evolution history and the function of KptA/Tpt1 from prokaryote to eukaryote organisms. At the same time, the results of promoter elements analysis were also shown in the present study. Moreover, the problems in the function of KptA/Tpt1 that have not been clarified at the present time are summarised, and some suggestions to solve those problems are given. This review presents no only a summary of clear function of KptA/Tpt1 in the process of tRNA splicing and ADP-ribosylation of organisms, but also gives some proposals to clarify unclear problems of it in the future.

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27

Pallett, Helen. "Situating organisational learning and public participation: Stories, spaces and connections." Transactions of the Institute of British Geographers 43, no. 2 (September 26, 2017): 215–29. http://dx.doi.org/10.1111/tran.12214.

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Mattes, Robert. "South Africans' participation in local politics and government." Transformation: Critical Perspectives on Southern Africa 66, no. 1 (2008): 117–41. http://dx.doi.org/10.1353/trn.0.0011.

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Ramos-Martinez, Espiridión, Ramcés Falfán-Valencia, Gloria Pérez-Rubio, Mayra Mejia, Ivette Buendía-Roldán, Montserrat I. González-Pérez, Heidegger N. Mateos-Toledo, and Jorge Rojas Serrano. "Anti-Aminoacyl Transfer-RNA-Synthetases (Anti-tRNA) Autoantibodies Associated with Interstitial Lung Disease: Pulmonary Disease Progression has a Persistent Elevation of the Th17 Cytokine Profile." Journal of Clinical Medicine 9, no. 5 (May 6, 2020): 1356. http://dx.doi.org/10.3390/jcm9051356.

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Anti-tRNA autoantibodies are associated with interstitial lung disease (ILD), in at least two clinical scenarios: the anti-synthetase syndrome (ASSD) and interstitial pneumonia with autoimmune features (IPAF). Under pathological conditions, cytokines indicate the participating elements and the course of inflammatory phenomena. We aimed to quantify serum concentrations of different inflammatory cytokines profiles in patients with anti-tRNA associated ILD (anti-tRNA-ILD) and estimate the association between these and ILD improvement and progression. Serum levels of 18 cytokines from baseline and after six months of treatment of ILD patients’ positives to anti-tRNA were included in the current study. At six months, patients were classified as with or without ILD progression. A total of 39 patients were included (10 anti-Jo1, eight anti-PL7, 11 anti-PL12, and 10 anti-Ej). Three patients (7.6%) had ILD progression (progressors patients, PP) and showed statistically higher levels in IL-4, IL-10, IL-17A, IL-22, GM-CSF, IL-1β, IL-6, IL-12, IL-18, and TNF-α, compared to patients without disease progression (no progressors patients, NPP). IL-17A, IL-1β, and IL-6 (T-helper-lymphocyte (Th)17 inflammatory cytokine profile) were elevated and had a high discriminatory capacity in distinguishing ILD PP of those NPP at follow-up. Overall, there is an association between the cytokines of the Th17 inflammatory profile and the ASSD progression.

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30

Bénit-Gbaffou, Claire. "Introduction: The place of participation in South African local democracy." Transformation: Critical Perspectives on Southern Africa 66, no. 1 (2008): i—vii. http://dx.doi.org/10.1353/trn.0.0001.

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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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Bénit-Gbaffou, Claire. "Are practices of local participation sidelining the institutional participatory channels?: Reflections from Johannesburg." Transformation: Critical Perspectives on Southern Africa 66, no. 1 (2008): 1–33. http://dx.doi.org/10.1353/trn.0.0003.

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Ballard, Richard. "Between the community hall and the city hall: five research questions on participation." Transformation: Critical Perspectives on Southern Africa 66, no. 1 (2008): 168–88. http://dx.doi.org/10.1353/trn.0.0004.

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34

Piper, Laurence, and Roger Deacon. "Party politics, elite accountability and public participation: Ward committee politics in the Msunduzi Municipality." Transformation: Critical Perspectives on Southern Africa 66, no. 1 (2008): 61–82. http://dx.doi.org/10.1353/trn.0.0007.

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Villet, R., M. Fonvielle, P. Busca, M. Chemama, A. P. Maillard, J. E. Hugonnet, L. Dubost, et al. "Idiosyncratic features in tRNAs participating in bacterial cell wall synthesis." Nucleic Acids Research 35, no. 20 (November 29, 2007): 6870–83. http://dx.doi.org/10.1093/nar/gkm778.

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36

Thompson, Lisa. "Public participation on dam building in South Africa: a case study of the Berg Water Project." Transformation: Critical Perspectives on Southern Africa 68, no. 1 (2008): 1–27. http://dx.doi.org/10.1353/trn.0.0021.

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Priestley, George. "Antillean-Panamanians or Afro-Panamanians?: Political Participation and the Politics of Identity During the Carter-Torrijos Treaty Negotiations." Transforming Anthropology 12, no. 1-2 (January 2004): 50–67. http://dx.doi.org/10.1525/tran.2004.12.1-2.50.

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38

Moyo, Bekezela, Teresa Dirsuweit, and Ann Cameron. "The limits of public participation in environmental impact assessment processes: the case of indigenous communities in Mapela, Limpopo Province." Transformation: Critical Perspectives on Southern Africa 94, no. 1 (2017): 28–50. http://dx.doi.org/10.1353/trn.2017.0011.

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39

Oda, Masataka, Syusuke Ikari, Takayuki Matsuno, Yuka Morimune, Masahiro Nagahama, and Jun Sakurai. "Signal Transduction Mechanism Involved in Clostridium perfringens Alpha-Toxin-Induced Superoxide Anion Generation in Rabbit Neutrophils." Infection and Immunity 74, no. 5 (May 2006): 2876–86. http://dx.doi.org/10.1128/iai.74.5.2876-2886.2006.

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ABSTRACT Clostridium perfringens alpha-toxin induces the generation of superoxide anion (O2 −) via production of 1,2-diacylglycerol (DG) in rabbit neutrophils. The mechanism of the generation, however, remains poorly understood. Here we report a novel mechanism for the toxin-induced production of O2 − in rabbit neutrophils. Treatment of the cells with the toxin resulted in tyrosine phosphorylation of a protein of about 140 kDa. The protein reacted with anti-TrkA (nerve growth factor high-affinity receptor) antibody and bound nerve growth factor. Anti-TrkA antibody inhibited the production of O2 − and binding of the toxin to the protein. The toxin induced phosphorylation of 3-phosphoinositide-dependent protein kinase 1 (PDK1). K252a, an inhibitor of TrkA receptor, and LY294002, an inhibitor of phosphatidylinositol 3-kinase (PI3K), reduced the toxin-induced production of O2 − and phosphorylation of PDK1, but not the formation of DG. These inhibitors inhibited the toxin-induced phosphorylation of protein kinase C θ (PKCθ). U73122, a phospholipase C (PLC) inhibitor, and pertussis toxin inhibited the toxin-induced generation of O2 − and formation of DG, but not the phosphorylation of PDK1. These observations show that the toxin independently induces production of DG through activation of endogenous PLC and phosphorylation of PDK1 via the TrkA receptor signaling pathway and that these events synergistically activate PKCθ in stimulating an increase in O2 −. In addition, we show the participation of mitogen-activated protein kinase-associated signaling events via activation of PKCθ in the toxin-induced generation of O2 −.

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40

Staniland, Luke. "'They know me, I will not get any job': public participation, patronage, and the sedation of civil society in a Capetonian township." Transformation: Critical Perspectives on Southern Africa 66, no. 1 (2008): 34–60. http://dx.doi.org/10.1353/trn.0.0005.

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Gökbulut, Özlem Dağlı, Burak Gökbulut, and Mustafa Yeniasır. "The impact of pandemic process on special education in Cyprus." LAPLAGE EM REVISTA 7, no. 2 (April 12, 2021): 364–84. http://dx.doi.org/10.24115/s2446-6220202172749p.364-384.

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In this paper, the education programs offered to students with special needs in the online distance education format during the Covid-19 pandemic period in TRNC and the online family guidance/counseling services offered to their families were evaluated from the perspective of the families. In the study, the data obtained follow a parallel course with other studies in the literature. In studies on the academic support provided by families for children and family participation in learning processes, the relation between family involvement at home and at school and academic success was revealed, which is also the case in this study. In addition, family involvement was determined as an essential predictor of the school success of students, and it was emphasized that increasing family participation would help education reach higher standards and students encounter alternative opportunities.

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42

Stahl, Guillaume, Samia N. Ben Salem, Lifeng Chen, Bing Zhao, and Philip J. Farabaugh. "Translational Accuracy during Exponential, Postdiauxic, and Stationary Growth Phases in Saccharomyces cerevisiae." Eukaryotic Cell 3, no. 2 (April 2004): 331–38. http://dx.doi.org/10.1128/ec.3.2.331-338.2004.

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ABSTRACT When the yeast Saccharomyces cerevisiae shifts from rapid growth on glucose to slow growth on ethanol, it undergoes profound changes in cellular metabolism, including the destruction of most of the translational machinery. We have examined the effect of this metabolic change, termed the diauxic shift, on the frequency of translational errors. Recoding sites are mRNA sequences that increase the frequency of translational errors, providing a convenient reporter of translational accuracy. We found that the diauxic shift causes no overall change in translational accuracy but does cause a strong reduction in the frequency of one type of programmed error: Ty +1 frameshifting. Genetic data suggest that this effect may be due to changes in the relative amounts of tRNA participating in translation elongation. We discuss possible implications for expression strategies that use recoding.

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Baştaş, Mert, and Hüseyin Aktunç. "The role of the leader in the institutional communication process in TRNC primary schools." Revista Tempos e Espaços em Educação 13, no. 32 (December 11, 2020): 1–15. http://dx.doi.org/10.20952/revtee.v13i32.14948.

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The general purpose of this research is the examination of the role of the leader in the institutional communication process in TRNC primary schools. While conducting the research, principals and deputy principals, who are administrators in primary schools, were accepted as leaders in schools. At this point, it has been tried to determine how teachers perceive corporate communication in TRNC primary schools and whether their administrators show a leading role in terms of communication skills. Among the most important results of the research; Primary school teachers with a bachelor's degree had a more positive attitude towards the communication skills of their administrators than primary school teachers with a master's degree. Most of the teachers (69.4%) participating in our study stated that the most important feature that a leader should have is "effective communication skills".

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Tran Thi Diem, Can, and Tron Nguyen Van. "THE SITUATION OF GENDER EQUALITY IN RURAL EDUCATION IN TRAN DE DISTRICT, SOC TRANG PROVINCE." Journal of Science Social Science 65, no. 11 (November 2020): 123–31. http://dx.doi.org/10.18173/2354-1067.2020-0077.

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The study was conducted to describe and analyze the situation of gender equality in education in Tran De district, Soc Trang province through descriptive statistical methods. The research results showed that gender equality activities in Tran De district, Soc Trang province have achieved many positive results, brought new prosperity to improve the lives of people in the district and women of ethnic minoritiesin particular, especially Khmer women. Females accounted for 47% of total educational staff. Out of a total of 99 managers at affiliated schools, 49 of them staff are female (49.49%). The leadership ability of females is also increasingly receiving recognition from many sides and in many fields. Women gradually have a position both in the family and in society, they have been participating in the socio-Economic Activities, and studying to improve People’s Educational Level.

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Godfrey, Shane, and Johann Maree. "Can government facilitate participative workplace change? An examination of the Workplace Challenge Project in the Cape fish processing industry." Transformation: Critical Perspectives on Southern Africa 62, no. 1 (2007): 30–58. http://dx.doi.org/10.1353/trn.2007.0005.

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Deichman, A. M. "Natural hypothetic oligonucleotide modifiers, activity regulators and theoretical minimal RNA rings ordering processes of expression and modification of genes / genome." Russian Journal of Biotherapy 21, no. 1 (April 13, 2022): 21–32. http://dx.doi.org/10.17650/1726-9784-2022-21-1-21-32.

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A special hypothetical mechanism of variable Individual Epitope Reverse Translation (at least 2 types) of eukaryotic cell is probably capable of reproducing primary linear (sens- / antisense-, CRISPR-, repeat-like, etc.) and secondary conformational (similar to quadruplexs, RNA-hairpins, RNA-ring-structures; etc.) oligonucleotide structures formed in the mitochondrial membrane-bound supramolecular and containing nanomolecular inclusions hypothetical particle of the retranslosome. This is the so-called nucleic acid equivalents of protein epitope, oligo-NEs, monomeric in ~15–30 and oligomeric in ~(15–30)n nucleotides, potentially capable of participating in the regulation of expression (activation, termination, switching) and modification of genes / genome, as well as in the creation protein / enzyme-containing nucleoprotein platform- / module- / complex-like formations in normal, pathologically altered (in particular, tumor) and virus-infected cells. Recently, in the GenBank databases, they are shown realistically and built / calculated bioinformatically in silico so-called minimum theoretical of 22 nucleotides and longer RNAring (stem-loop) structures, the composition of which depends, firstly, on constantly occurring chemical and enzymatic processes (including deamination mutations), and the properties of which, secondly, link, respectively, with the early (era of the so-called circular code) and later (era of modern universal coding, including the circular code as a component) evolutionary periods of the formation of the whole genetic code. It is generally accepted that the emergence and formation, respectively, of early evolutionary (proto-tRNA, proto-rRNA) and modern variants of molecules of the translational machine of mitochondria and cytoplasm is associated with stem-loop RNA-ring structures, similar to independently proposed oligo-NEs, such as tRNA, rRNA and gene products of ribosomal and other proteins.

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Fu, Jianming, Ivana Momčilović, and P. V. Vara Prasad. "Roles of Protein Synthesis Elongation Factor EF-Tu in Heat Tolerance in Plants." Journal of Botany 2012 (June 3, 2012): 1–8. http://dx.doi.org/10.1155/2012/835836.

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EF-Tu proteins of plastids, mitochondria, and the cytosolic counterpart EF-1α in plants, as well as EF-Tu proteins of bacteria, are highly conserved and multifunctional. The functions of EF-Tu include transporting the aminoacyl-tRNA complex to the A site of the ribosome during protein biosynthesis; chaperone activity in protecting other proteins from aggregation caused by environmental stresses, facilitating renaturation of proteins when conditions return to normal; displaying a protein disulfide isomerase activity; participating in the degradation of N-terminally blocked proteins by the proteasome; eliciting innate immunity and triggering resistance to pathogenic bacteria in plants; participating in transcription when an E. coli host is infected with phages. EF-Tu genes are upregulated by abiotic stresses in plants, and EF-Tu plays important role in stress responses. Expression of a plant EF-Tu gene confers heat tolerance in E. coli, maize knock-out EF-Tu null mutants are heat susceptible, and over-expression of an EF-Tu gene improves heat tolerance in crop plants. This review paper summarizes the current knowledge of EF-Tu proteins in stress responses in plants and progress on application of EF-Tu for developing crop varieties tolerant to abiotic stresses, such as high temperatures.

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Meyer, Michael A. "The Career of a Mediator. Manuel Joël, Conservative Liberal." transversal 14, no. 2 (December 30, 2016): 56–64. http://dx.doi.org/10.1515/tra-2016-0008.

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AbstractThis essay focuses upon Rabbi Manuel Joël, stressing for the first time his unusual position between the Positive-Historical and the Liberal movements within German Judaism. His stance produced controversy both with the Liberal Rabbi Abraham Geiger, his predecessor in the Breslau rabbinate, and Heinrich Graetz, his teacher at the Positive-Historical Breslau Theological Seminary. Points of dispute included Joël’s prayer book and his participation in the Liberal Leipzig Synod of 1869. Yet controversy eventually gave way to reconciliation and Joël could ultimately enjoy the respect of both factions.

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Toran, Mehmet. "An Analysis of Preschool Teachers’ Sense of Efficacy: A Case of TRNC." Journal of Education and Training Studies 5, no. 4 (March 10, 2017): 121. http://dx.doi.org/10.11114/jets.v5i4.2171.

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Determining the factors that affect teachers' competences has a decisive role in revealing the quality of teaching process. In this context, it is important to identify professional variables affecting the self-efficacy of preschool teachers. For this reason, it is aimed to investigate which professional variables influence preschool teachers' sense of efficacy. In the research, a descriptive research model was adopted. The working group of the study is composed of 191 preschool teachers participating in public nurseries and kindergartens in the TRNC, and also those participating to the research as a volunteer. The Professional Information Form and the Teacher’s Sense of Efficacy Scale were used as data collection tools in the study. Statistical analyses suitable for the analysis of the data were applied by applying the normality tests to the collected data. According to the findings obtained from the analysis made, except for the school type the preschool teachers graduated and the number of children, factors such as the graduated department, the place of residence, the duration of professional experience, the economic competence, and the educational environment were found to affect the self-efficacy of preschool teachers. As a result, it can be said that preschool teachers' self-efficacy is influenced by professional variables.

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Lutz, W. H., and K. L. Barker. "Effect of estradiol on the amino acid-accepting activity of uterine tRNAs and their participation in protein synthesis." Journal of Biological Chemistry 261, no. 24 (August 1986): 11230–35. http://dx.doi.org/10.1016/s0021-9258(18)67372-7.

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Journal articles on the topic 'TRNA Participation'

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