TRNA modification

Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, et al. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure 2004 12 593-602. 

Tsui, H. C., Feng, G., and Winkler, M. E. (1996). Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered Esigma32-specific promoters during heat shock. J. Bacteriol. 178, 5719—5731. 

In addition to the variety of modifications found on the heterocyclic base discussed above, many nucleosides are also methylated at the 2 -hydroxyl of the ribose moiety and make up approximately 8 % of existing tRNA modifications. One interesting example of the 2 - 0-ribose modification was studied in S. cerevisiae, where the yeast tRNA molecules corresponding to His, Pro, and Gly(G-C-C) contain a 2 -0-methylated nucleoside at position 4 in the acceptor stem. A methylated cytosine is found in tRNA ° and tRNA, and the modified Am nucleoside is found in tRNA . Modifications in a duplex region of tRNA are very rare, yet modification at this position ( 4) is conserved in eukaryotes. A yeast knock-out strain of the gene trmlS was produced, and it was determined by HPLC and primer extension analysis that tRNAs purified from this organism did not exhibit the 2 - 0-methyl modification at position 4. 

Recently, the gene cinQJmm the a A.g copper-inducible operon from Pseudomonasputida has been shown to exhibit preQ oxidoreductase activityAlthough part of a copper-inducible operon, insertional disruption of the .Q gene did not demonstrate a link to copper sensitivity. However, additional studies are required to further probe this link between tRNA modification and copper homeostasis. 

Enzymes in the radical SAM superfamily carry out a diverse set of reactions including sulfur insertion in biotin and lipoate synthases, DNA repair, tRNA modification, and are involved in the synthesis of molybdop-terin, heme, thiamine, and many natural products. Shepard and Broderick discuss the common themes in these reactions and differentiating details in the chapter. Despite the diversity of the reactions, they all begin with a... 

Noon KR, Guymon R, Crain PL, McCloskey JA, Thomm M, Lim J, Cavicchioli R. Influence of temperature on tRNA modification in archaea Metanococcides burtonii optimum growth temperature (Topt 23°C) and Stetteria hydrogenophila (Topt 95°C). J Bacteriol. 2003 5483-5490. 

Wei FY, Tomizawa K. Functional loss of Cdkall, a novel tRNA modification enzyme, causes the development of type 2 diabetes. Endocr J. 2011 58 819-25. 

A -Threonylcarbamoyladenosine (t A) is a hypermodified nucleotide found in decoding codons of some tRNAs, and the endopeptidase-like kinase chromatin associated receptor (EKC/KEOPS) is a conserved complex involved in many cellular processes in archaea and eukarya. Mutational analysis of EKC/KEOPS revealed a direct role of the eomplex in tRNA modification. A -Methyladenosine has also been shown to be a major factor in fat mass and obesity-associated protein (FTO). As was found with the corresponding A -cytidine derivative, eagjng of adenosine with A -nitrodibenzofuran led to deprotection up to 12 times more efficiently than the more commonly used NPE photo-label, and it was specifically removed by irradiation at 365 nm. ... 

Posttranslational modification of preformed polynucleotides can generate additional bases such as pseudouridine, in which D-ribose is linked to C-5 of uracil by a carbon-to-carbon bond rather than by a P-N-glycosidic bond. The nucleotide pseudouridylic acid T arises by rearrangement of UMP of a preformed tRNA. Similarly, methylation by S-adenosylmethionine of a UMP of preformed tRNA forms TMP (thymidine monophosphate), which contains ribose rather than de-oxyribose. 

Aminoacyl-tRNA synthetases Degradation of proteins, peptides, and glycopeptides Nucleoproteins Protein modification... 

The fluorescence decay is multiexponential.(199 200) This is unequivocal evidence that the wyebutine base can be bound in at least two different conformations with different solvent shielding. Wells and Lakowicz(200) resolved two exponential components. They measured the normalized amplitudes and lifetimes for the wyebutine fluorescence at two different concentrations of added Mg2+ S° = 0.50, t, = 1.7 ns, = 0.50, and t2 = 5.9 ns with no added Mg2+ present, and S°i = 0.16, t, =0.6 ns, S2 = 0.84, and r2 = 6.0ns with 10 nM Mg2+. Since the 6ns component is the longest lifetime present, it must represent the conformation that shields the wyebutine to the greatest extent and is generally believed to involve a 3 stack of bases 34-38.w 199-2011 The fraction of the tRNA in this conformation increases when Mg2 + is added to the solution. This structure is also observed in crystal structures which include Mg2+.(202 204) In the other conformation(s), the wyebutine is more exposed to the solvent. A 5 stack, which does not include bases 37 and 38, is one possibility. The wyebutine base would be more exposed to the solvent and have a shorter fluorescence lifetime as a result. However, both NMR data(205 206) and chemical modification studies(207) are inconsistent with a 5 stack. For the moment, this matter is unresolved. 

Clearly, the results emerging suggested that at least two nucleotides were modified, the absolute sequence position within the tRNA had yet to be established. Ching etalP showed that a Se U residue was present in the wobble position of the tRNA " from C. sticklandii. This study confirmed a notion that the modification probably affects the translation efficiency of certain transcripts, based on the level of modification by selenium. The authors speculated that the modification to seleno-tRNA (GAG) allowed for more efficient use of this tRNA species as compared to the tRNA (GAA). Even today, no definitive data exist to show that this modification alters the translation efficiency in these bacterial model systems. Nonetheless, these studies had established the chemical forms of Se U and mnm Se U, and established that they were derived from modifications to nucleotides that first required sulfur (S U and mnm S U), the mechanism by which selenium was inserted into the tRNA would not be definitively answered until many years later. 

Figure 4 Recognition elements of tRNA° ". Highlighted in blue with bars are the recognition elements for Gln-tRNA° " synthesis by GatCAB and GatDE. The U1-A72 base pair is a common identity element, while antideterminants for noncognate tRNAs are scanned for in the D-loop. Highlighted in magenta are the identity elements of tRNA° " for GlnRS.tRNA " from Bacillus subtilis is shown, but base modifications at positions 32-38 and 33-37 allow base pairing in E. coll tRNA " .

Gml8, s T54, and m A58. " " ° Combination of these modifications is not found in other prokaryotic tRNAs. It has been shown that they reinforce the thermostability of the tRNAs of T. thermophilus by increasing the by... 

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