Non-nucleotide Modification of Anti-miRNA Oligonucleotides

2016 ◽  
pp. 51-69 ◽  
Author(s):  
Kim A. Lennox ◽  
Christopher A. Vakulskas ◽  
Mark A. Behlke
Keyword(s):  
Nucleotide Modification

scholarly journals RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea

2004 ◽  
Vol 54 (4) ◽  
pp. 980-993 ◽  
Author(s):  
Sonia M. Ziesche ◽  
Arina D. Omer ◽  
Patrick P. Dennis
Keyword(s):  
Ribosomal Rnas ◽  
Nucleotide Modification

Nucleotide Modification, A Radical Mechanism of Oxidative Toxicity

1986 ◽  
Vol 2 (3) ◽  
pp. 129-136 ◽  
Author(s):  
Carl Bernofsky ◽  
Sean W. O'dea
Keyword(s):  
Radical Mechanism ◽  
Nucleotide Modification

scholarly journals Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
W. S. Vincent Yip ◽  
Nicholas G. Vincent ◽  
Susan J. Baserga
Keyword(s):  
Ribosome Biogenesis ◽  
Gene Organization ◽  
Rrna Gene ◽  
Rrna Processing ◽  
Ribosomal Rnas ◽  
Intensive Research ◽  
Complex Process ◽  
Nucleotide Modification

Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.

scholarly journals Reassessment of Viroid RNA Cytosine Methylation Status at the Single Nucleotide Level

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 357
Author(s):  
Francesco Di Serio ◽  
Enza Maria Torchetti ◽  
José-Antonio Daròs ◽  
Beatriz Navarro
Keyword(s):  
Cytosine Methylation ◽  
Methylation Status ◽  
Potato Spindle Tuber Viroid ◽  
Nucleotide Level ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Nucleotide Modification ◽  
Rna Structural Motifs ◽  
Infectious Cycle ◽  
Positive Results

Composed of a few hundreds of nucleotides, viroids are infectious, circular, non-protein coding RNAs able to usurp plant cellular enzymes and molecular machineries to replicate and move in their hosts. Several secondary and tertiary RNA structural motifs have been implicated in the viroid infectious cycle, but whether modified nucleotides, such as 5C-methylcytosine (m5C), also play a role has not been deeply investigated so far. Here, the possible existence of m5C in both RNA polarity strands of potato spindle tuber viroid and avocado sunblotch viroid -which are representative members of the nucleus- and chloroplast-replicating viroids, respectively- has been assessed at single nucleotide level. We show that a standard bisulfite protocol efficiently used for identifying m5C in cellular RNAs may generate false positive results in the case of the highly structured viroid RNAs. Applying a bisulfite conversion protocol specifically adapted to RNAs with high secondary structure, no m5C was identified in both polarity strands of both viroids, indicating that this specific nucleotide modification does not likely play a role in viroid biology.

Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem

Chromosoma ◽  
1997 ◽  
Vol 105 (7-8) ◽  
pp. 391-400 ◽  
Author(s):  
B. Edward H. Maden ◽  
John M. X. Hughes
Keyword(s):  
Ribosomal Rna ◽  
Nucleotide Modification

scholarly journals Cicada endosymbionts contain tRNAs that are processed despite having genomes that lack tRNA processing activities

2018 ◽  
Author(s):  
James T. Van Leuven ◽  
Meng Mao ◽  
Gordon M. Bennett ◽  
John P. McCutcheon
Keyword(s):  
Trna Synthetase ◽  
Essential Genes ◽  
Trna Processing ◽  
Cellular Processes ◽  
Endosymbiotic Bacteria ◽  
Nucleotide Modification ◽  
Computational Annotation ◽  
Genes Encoding ◽  
Trna Halves ◽  
Computational Predictions

Gene loss and genome reduction are defining characteristics of nutritional endosymbiotic bacteria. In extreme cases, even essential genes related to core cellular processes such as replication, transcription, and translation are lost from endosymbiont genomes. Computational predictions on the genomes of the two bacterial symbionts of the cicadaDiceroprocta semicincta, “CandidatusHodgkinia cicadicola” (Alphaproteobacteria) and “Ca. Sulcia muelleri” (Betaproteobacteria), find only 26 and 16 tRNA, and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original “Ca.Hodgkinia” genome annotation is missing several essential genes involved in tRNA processing, such as RNase P and CCA tRNA nucleotidyltransferase, as well as several RNA editing enzymes required for tRNA maturation. How “Ca. Sulcia” and “Ca. Hodgkinia” preform basic translation-related processes without these genes remains unknown. Here, by sequencing eukaryotic mRNA and total small RNA, we show that the limited tRNA set predicted by computational annotation of “Ca. Sulcia” and “Ca. Hodgkinia” is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5’ and 3’ ends, and seem to undergo nucleotide modification. Surprisingly, we find that most “Ca. Hodgkinia”and “Ca. Sulcia” tRNAs exist as tRNA halves. Finally, and in contrast with other related insects, we show that cicadas have experienced little horizontal gene transfer that might complement the activities missing from the endosymbiont genomes. We conclude that “Ca. Sulcia” and “Ca. Hodgkinia” tRNAs likely function in bacterial translation, but require host-encoded enzymes to do so.

19 Nucleotide Modification in RNA

1982 ◽  
pp. 567-582 ◽  
Author(s):  
Larry K. Kline ◽  
Dieter Söll
Keyword(s):  
Nucleotide Modification

scholarly journals Nucleotide Modification Alters MicroRNA-Dependent Silencing of MicroRNA Switches

2019 ◽  
Vol 14 ◽  
pp. 339-350 ◽  
Author(s):  
John Lockhart ◽  
John Canfield ◽  
Ezinne Francess Mong ◽  
Jeffrey VanWye ◽  
Hana Totary-Jain
Keyword(s):  
Nucleotide Modification

scholarly journals Pseudouridine Synthase RsuA Captures an Assembly Intermediate That Is Stabilized by Ribosomal Protein S17

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 841
Author(s):  
Kumudie Jayalath ◽  
Sean Frisbie ◽  
Minhchau To ◽  
Sanjaya Abeysirigunawardena
Keyword(s):  
Ribosomal Protein ◽  
Ribosome Biogenesis ◽  
Small Subunit ◽  
Pseudouridine Synthase ◽  
Cellular Events ◽  
Complex Process ◽  
Nucleotide Modification ◽  
Living Organisms ◽  
Assembly Intermediate ◽  
Peripheral Domain

The ribosome is a large ribonucleoprotein complex that synthesizes protein in all living organisms. Ribosome biogenesis is a complex process that requires synchronization of various cellular events, including ribosomal RNA (rRNA) transcription, ribosome assembly, and processing and post-transcriptional modification of rRNA. Ribosome biogenesis is fine-tuned with various assembly factors, possibly including nucleotide modification enzymes. Ribosomal small subunit pseudouridine synthase A (RsuA) pseudouridylates U516 of 16S helix 18. Protein RsuA is a multi-domain protein that contains the N-terminal peripheral domain, which is structurally similar to the ribosomal protein S4. Our study shows RsuA preferably binds and pseudouridylates an assembly intermediate that is stabilized by ribosomal protein S17 over the native-like complex. In addition, the N-terminal domain truncated RsuA showed that the presence of the S4-like domain is important for RsuA substrate recognition.

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