Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing [PDF]
Frontiers in Molecular Biosciences, 2022 RNA ligases play important roles in repairing and circularizing RNAs post-transcriptionally. In this study, we generated an allelic knockout of ATP-dependent RNA ligase (Rnl) in the hyperthermophilic archaeon Thermococcus kodakarensis to identify its biological targets.
Yancheng Liu +7 more
doaj +5 more sources
Cleavage of 3′-terminal adenosine by archaeal ATP-dependent RNA ligase [PDF]
Scientific Reports, 2017 AbstractMethanothermobacter thermoautotrophicus RNA ligase (MthRnl) catalyzes formation of phosphodiester bonds between the 5′-phosphate and 3′-hydroxyl termini of single-stranded RNAs. It can also react with RNA with a 3′-phosphate end to generate a 2′,3′-cyclic phosphate.
Yancheng Liu +4 more
core +7 more sources
Synthesis of bisphosphonate derivatives of ATP by T4 RNA ligase [PDF]
FEBS Letters, 2006 T4 RNA ligase catalyzes the synthesis of ATP β,γ‐bisphosphonate analogues, using the following substrates with the relative velocity rates indicated between brackets: methylenebisphosphonate (pCH2p) (100), clodronate (pCCl2p) (52), and etidronate (pC(OH)(CH3)p) (4). The presence of pyrophosphatase about doubled the rate of these syntheses. Pamidronate (
Günther Sillero, María A. +4 more
openaire +6 more sources
Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis [PDF]
Nucleic Acids Research, 2016 An ATP-dependent RNA ligase from Methanobacterium thermoautotrophicum (MthRnl) catalyzes intramolecular ligation of single-stranded RNA to form a closed circular RNA via covalent ligase-AMP and RNA-adenylylate intermediate. Here, we report the X-ray crystal structures of an MthRnl•ATP complex as well as the covalent MthRnl-AMP intermediate.
Raka Ghosh +7 more
openaire +4 more sources
Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase – engineering a thermostable ATP independent enzyme [PDF]
BMC Molecular Biology, 2012 RNA ligases are essential reagents for many methods in molecular biology including NextGen RNA sequencing. To prevent ligation of RNA to itself, ATP independent mutant ligases, defective in self-adenylation, are often used in combination with activated pre-adenylated linkers.
Larry A. McReynolds +1 more
openaire +5 more sources
Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2 [PDF]
BMC Structural Biology, 2015 RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology.
Sandrine Moreira +3 more
openaire +4 more sources
Synthesis of ATP derivatives of compounds of the mevalonate pathway (isopentenyl di- and triphosphate; geranyl di- and triphosphate, farnesyl di- and triphosphate, and dimethylallyl diphosphate) catalyzed by T4 RNA ligase, T4 DNA ligase and other ligases [PDF]
Biochemical Pharmacology, 2009 Compounds of the mevalonate pathway containing a terminal di- or triphosphate (mev-PP or mev-PPP) were tested as substrates of several enzyme ligases (T4 RNA ligase, T4 DNA ligase, firefly luciferase and other ligases) for the synthesis of ATP derivatives of the mev-pppA or mev-ppppA type.
Francisco J. Pérez-Zúñiga +5 more
openaire +6 more sources
Adaptive remodeling of the bacterial proteome by specific ribosomal modification regulates Pseudomonas infection and niche colonisation [PDF]
, 2016 Post-transcriptional control of protein abundance is a highly important, underexplored regulatory process by which organisms respond to their environments.
A Brencic +83 more
core +8 more sources
Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4 [PDF]
, 2006 The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of ...
Amitsur +61 more
core +4 more sources
HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. [PDF]
, 2006 microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants bear a methyl group on the ribose of the 3' terminal nucleotide. We showed previously that the methylation of miRNAs and siRNAs requires the protein HEN1 in vivo and that purified HEN1 ...
Chen, Xuemei +3 more
core +2 more sources