keyword
MENU ▼
Read by QxMD icon Read
search

tRNA methylation

keyword
https://www.readbyqxmd.com/read/28230814/m1a%C3%A2-post-transcriptional%C3%A2-modification%C3%A2-in%C3%A2-trnas
#1
REVIEW
Stephanie Oerum, Clément Dégut, Pierre Barraud, Carine Tisné
To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230119/editing-and-methylation-at-a-single-site-by-functionally-interdependent-activities
#2
Mary Anne T Rubio, Kirk W Gaston, Katherine M McKenney, Ian M C Fleming, Zdeněk Paris, Patrick A Limbach, Juan D Alfonzo
Nucleic acids undergo naturally occurring chemical modifications. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified. Despite recent progress, the mechanism for the biosynthesis of most modifications is not fully understood, owing, in part, to the difficulty associated with reconstituting enzyme activity in vitro. Whereas some modifications can be efficiently formed with purified components, others may require more intricate pathways...
February 22, 2017: Nature
https://www.readbyqxmd.com/read/28218716/sulfur-modifications-of-the-wobble-u34-in-trnas-and-their-intracellular-localization-in-eukaryotic-cells
#3
REVIEW
Yumi Nakai, Masato Nakai, Takato Yano
The wobble uridine (U34) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNA(Lys)UUU, tRNA(Glu)UUC, and tRNA(Gln)UUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U34, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U34 (s²U34) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations...
February 18, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208788/next-generation%C3%A2-sequencing-based%C3%A2-ribomethseq%C3%A2-protocol%C3%A2-for%C3%A2-analysis%C3%A2-of%C3%A2-trna%C3%A2-2-o-methylation
#4
Virginie Marchand, Florian Pichot, Kathrin Thüring, Lilia Ayadi, Isabel Freund, Alexander Dalpke, Mark Helm, Yuri Motorin
Analysis of RNA modifications by traditional physico-chemical approaches is labor  intensive,  requires  substantial  amounts  of  input  material  and  only  allows  site-by-site  measurements.  The  recent  development  of  qualitative  and  quantitative  approaches  based  on   next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA  species.  The  Illumina  sequencing-based  RiboMethSeq  protocol  was  initially  developed  and  successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations...
February 9, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208632/cross-talk-between-dnmt2-dependent-trna-methylation-and-queuosine-modification
#5
REVIEW
Ann E Ehrenhofer-Murray
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S...
February 10, 2017: Biomolecules
https://www.readbyqxmd.com/read/28205560/alkb-homolog-3-mediated-trna-demethylation-promotes-protein-synthesis-in-cancer-cells
#6
Yuko Ueda, Ikumi Ooshio, Yasuyuki Fusamae, Kaori Kitae, Megumi Kawaguchi, Kentaro Jingushi, Hiroaki Hase, Kazuo Harada, Kazumasa Hirata, Kazutake Tsujikawa
The mammalian AlkB homolog (ALKBH) family of proteins possess a 2-oxoglutarate- and Fe(II)-dependent oxygenase domain. A similar domain in the Escherichia coli AlkB protein catalyzes the oxidative demethylation of 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) in both DNA and RNA. AlkB homolog 3 (ALKBH3) was also shown to demethylate 1-meA and 3-meC (induced in single-stranded DNA and RNA by a methylating agent) to reverse the methylation damage and retain the integrity of the DNA/RNA. We previously reported the high expression of ALKBH3 in clinical tumor specimens and its involvement in tumor progression...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28134793/trm112-a-protein-activator-of-methyltransferases-modifying-actors-of-the-eukaryotic-translational-apparatus
#7
REVIEW
Gabrielle Bourgeois, Juliette Létoquart, Nhan van Tran, Marc Graille
Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation...
January 27, 2017: Biomolecules
https://www.readbyqxmd.com/read/28119416/human-bcdin3d-monomethylates-cytoplasmic-histidine-transfer-rna
#8
Anna Martinez, Seisuke Yamashita, Takashi Nagaike, Yuriko Sakaguchi, Tsutomu Suzuki, Kozo Tomita
Human RNA methyltransferase BCDIN3D is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. Here, we show that cytoplasmic tRNA(His) is the primary target of BCDIN3D in human cells. Recombinant human BCDIN3D, expressed in Escherichia coli, monomethylates the 5'-monophosphate of cytoplasmic tRNA(His) efficiently in vitro In BCDN3D-knockout cells, established by CRISPR/Cas9 editing, the methyl moiety at the 5'-monophosphate of cytoplasmic tRNA(His) is lost, and the exogenous expression of BCDIN3D in the knockout cells restores the modification in cytoplasmic tRNA(His) BCIDN3D recognizes the 5'-guanosine nucleoside at position -1 (G-1) and the eight-nucleotide acceptor helix with the G-1-A73 mis-pair at the top of the acceptor stem of cytoplasmic tRNA(His), which are exceptional structural features among cytoplasmic tRNA species...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108655/the-novel-lysine-specific-methyltransferase-mettl21b-affects-mrna-translation-through-inducible-and-dynamic-methylation-of-lys-165-in-human-eukaryotic-elongation-factor-1-alpha-eef1a
#9
Jędrzej Małecki, Vinay Kumar Aileni, Angela Y Y Ho, Juliane Schwarz, Anders Moen, Vigdis Sørensen, Benedikt S Nilges, Magnus E Jakobsson, Sebastian A Leidel, Pål Ø Falnes
Lysine methylation is abundant on histone proteins, representing a dynamic regulator of chromatin state and gene activity, but is also frequent on many non-histone proteins, including eukaryotic elongation factor 1 alpha (eEF1A). However, the functional significance of eEF1A methylation remains obscure and it has remained unclear whether eEF1A methylation is dynamic and subject to active regulation. We here demonstrate, using a wide range of in vitro and in vivo approaches, that the previously uncharacterized human methyltransferase METTL21B specifically targets Lys-165 in eEF1A in an aminoacyl-tRNA- and GTP-dependent manner...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28103231/correction-mitochondrial-16s-rrna-is-methylated-by-trna-methyltransferase-trmt61b-in-all-vertebrates
#10
Dan Bar-Yaacov, Idan Frumkin, Yuka Yashiro, Takeshi Chujo, Yuma Ishigami, Yonatan Chemla, Amit Blumberg, Orr Schlesinger, Philipp Bieri, Basil Greber, Nenad Ban, Raz Zarivach, Lital Alfonta, Yitzhak Pilpel, Tsutomu Suzuki, Dan Mishmar
[This corrects the article DOI: 10.1371/journal.pbio.1002557.].
January 2017: PLoS Biology
https://www.readbyqxmd.com/read/28091672/a-rapid-way-to-discover-nonstandard-macrocyclic-peptide-modulators-of-drug-targets
#11
Toby Passioura, Hiroaki Suga
Studies of the fundamental nature of RNA catalysis and the potential mechanism of a shift from the "RNA world" to proteinaceous life lead us to identify a set of ribozymes (flexizymes) capable of promiscuous tRNA acylation. Whilst theoretically and mechanistically interesting in their own right, flexizymes have turned out to have immense practical value for the simple synthesis of tRNAs acylated with unusual amino acids, which in turn can be used for the ribosomal synthesis of peptides containing non-canonical residues...
January 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28041877/cytosine-5-rna-methylation-regulates-neural-stem-cell-differentiation-and%C3%A2-motility
#12
Joana V Flores, Lucía Cordero-Espinoza, Feride Oeztuerk-Winder, Amanda Andersson-Rolf, Tommaso Selmi, Sandra Blanco, Jignesh Tailor, Sabine Dietmann, Michaela Frye
Loss-of-function mutations in the cytosine-5 RNA methylase NSUN2 cause neurodevelopmental disorders in humans, yet the underlying cellular processes leading to the symptoms that include microcephaly remain unclear. Here, we show that NSUN2 is expressed in early neuroepithelial progenitors of the developing human brain, and its expression is gradually reduced during differentiation of human neuroepithelial stem (NES) cells in vitro. In the developing Nsun2(-/-) mouse cerebral cortex, intermediate progenitors accumulate and upper-layer neurons decrease...
January 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/27902775/determinants-of-trna-recognition-by-the-radical-sam-enzyme-rlmn
#13
Christina M Fitzsimmons, Danica Galonić Fujimori
RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets...
2016: PloS One
https://www.readbyqxmd.com/read/27870114/the-molecular-genetics-of-autosomal-recessive-nonsyndromic-intellectual-disability-a-mutational-continuum-and-future-recommendations
#14
REVIEW
Muzammil Ahmad Khan, Saadullah Khan, Christian Windpassinger, Muhammad Badar, Zafar Nawaz, Ramzi M Mohammad
Intellectual disability (ID) is a clinical manifestation of the central nervous system without any major dysmorphologies of the brain. Biologically it affects learning capabilities, memory, and cognitive functioning. The basic defining features of ID are characterized by IQ<70, age of onset before 18 years, and impairment of at least two of the adaptive skills. Clinically it is classified in a syndromic (with additional abnormalities) and a nonsyndromic form (with only cognitive impairment). The study of nonsyndromic intellectual disability (NSID) can best explain the pathophysiology of cognition, intelligence and memory...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27852927/evolution-of-trnaphe-img2-methyltransferases-involved-in-the-biosynthesis-of-wyosine-derivatives-in-archaea
#15
Jaunius Urbonavičius, Rasa Rutkienė, Anželika Lopato, Daiva Tauraitė, Jonita Stankevičiūtė, Agota Aučynaitė, Laura Kaliniene, Herman van Tilbeurgh, Rolandas Meškys
Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNA(Phe) In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N(1)-methylation of guanosine to yield m(1)G; and C(7)-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity...
December 2016: RNA
https://www.readbyqxmd.com/read/27849575/mg2-regulates-transcription-of-mgta-in-salmonella-typhimurium-via-translation-of-proline-codons-during-synthesis-of-the-mgtl-peptide
#16
Aaron R Gall, Kirill A Datsenko, Nara Figueroa-Bossi, Lionello Bossi, Isao Masuda, Ya-Ming Hou, Laszlo N Csonka
In Salmonella enterica serovar Typhimurium, Mg(2+) limitation induces transcription of the mgtA Mg(2+) transport gene, but the mechanism involved is unclear. The 5' leader of the mgtA mRNA contains a 17-codon, proline-rich ORF, mgtL, whose translation regulates the transcription of mgtA [Park S-Y et al. (2010) Cell 142:737-748]. Rapid translation of mgtL promotes formation of a secondary structure in the mgtA mRNA that permits termination of transcription by the Rho protein upstream of mgtA, whereas slow or incomplete translation of mgtL generates a different structure that blocks termination...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27819523/the-rna-methyltransferase-dnmt2-methylates-dna-in-the-structural-context-of-a-trna
#17
Steffen Kaiser, Tomasz P Jurkowski, Stefanie Kellner, Dirk Schneider, Albert Jeltsch, Mark Helm
The amino acid sequence of Dnmt2 is very similar to the catalytic domains of bacterial and eukaryotic DNA-(cytosine 5)-methyltransferases, but it efficiently catalyzes tRNA methylation, while its DNA methyltransferase activity is the subject of controversial reports with rates varying between zero and very weak. By using composite nucleic acid molecules as substrates, we surprisingly found that DNA fragments, when presented as covalent DNA-RNA hybrids in the structural context of a tRNA, can be more efficiently methylated than the corresponding natural tRNA substrate...
November 7, 2016: RNA Biology
https://www.readbyqxmd.com/read/27805064/comprehensive-dna-methylation-analysis-of-the-aedes-aegypti-genome
#18
Cassandra Falckenhayn, Vitor Coutinho Carneiro, Anderson de Mendonça Amarante, Katharina Schmid, Katharina Hanna, Seokyoung Kang, Mark Helm, George Dimopoulos, Marcelo Rosado Fantappié, Frank Lyko
Aedes aegypti mosquitoes are important vectors of viral diseases. Mosquito host factors play key roles in virus control and it has been suggested that dengue virus replication is regulated by Dnmt2-mediated DNA methylation. However, recent studies have shown that Dnmt2 is a tRNA methyltransferase and that Dnmt2-dependent methylomes lack defined DNA methylation patterns, thus necessitating a systematic re-evaluation of the mosquito genome methylation status. We have now searched the Ae. aegypti genome for candidate DNA modification enzymes...
November 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27791159/avilamycin-and-evernimicin-induce-structural-changes-in-rproteins-ul16-and-ctc-that-enhance-the-inhibition-of-a-site-trna-binding
#19
Miri Krupkin, Itai Wekselman, Donna Matzov, Zohar Eyal, Yael Diskin Posner, Haim Rozenberg, Ella Zimmerman, Anat Bashan, Ada Yonath
Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics...
November 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27769719/analysis-of-the-cleavage-mechanism-by-protein-only-rnase-p-using-precursor-trna-substrates-with-modifications-at-the-cleavage-site
#20
Dennis Walczyk, Markus Gößringer, Walter Rossmanith, Timofei S Zatsepin, Tatiana S Oretskaya, Roland K Hartmann
Ribonuclease P (RNase P) is the enzyme that endonucleolytically removes 5'-precursor sequences from tRNA transcripts in all domains of life. RNase P activities are either ribonucleoprotein (RNP) or protein-only RNase P (PRORP) enzymes, raising the question about the mechanistic strategies utilized by these architecturally different enzyme classes to catalyze the same type of reaction. Here, we analyzed the kinetics and cleavage-site selection by PRORP3 from Arabidopsis thaliana (AtPRORP3) using precursor tRNAs (pre-tRNAs) with individual modifications at the canonical cleavage site, with either Rp- or Sp-phosphorothioate, or 2'-deoxy, 2'-fluoro, 2'-amino, or 2'-O-methyl substitutions...
December 4, 2016: Journal of Molecular Biology
keyword
keyword
120664
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"