Pseudouridine in RNA: what, where, how, and why, IUBMB Life, vol.49, pp.341-351, 2000. ,
RNA pseudouridylation: new insights into an old modification, Trends Biochem. Sci, vol.38, pp.210-218, 2013. ,
Pseudouridine: still mysterious, but never a fake (uridine)! RNA Biol, vol.11, pp.1540-1554, 2014. ,
Stabilization of RNA stacking by pseudouridine, Nucleic Acids Res, vol.23, pp.5020-5026, 1995. ,
Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure, Biochemistry, vol.33, pp.7560-7567, 1994. ,
Investigation of Overhauser effects between pseudouridine and water protons in RNA helices, Proc. Natl. Acad. Sci. USA 99, pp.12697-12702, 2002. ,
1H-15N NMR studies of Escherichia coli tRNA(Phe) from hisT mutants: a structural role for pseudouridine, Biochemistry, vol.30, pp.4223-4231, 1991. ,
The contribution of pseudouridine to stabilities and structure of RNAs, Nucleic Acids Res, vol.42, pp.3492-3501, 2014. ,
Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations, Nucleic Acids Res, vol.42, pp.3971-3981, 2014. ,
, Scientific RepoRts |, vol.8, 2018.
Structural and functional roles of the N1-and N3-protons of psi at tRNA's position 39, Nucleic Acids Res, vol.27, pp.3543-3549, 1999. ,
Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine, J. Mol. Biol, vol.285, pp.115-131, 1999. ,
Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency, J. Biol. Chem, vol.277, pp.30445-30453, 2002. ,
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy, Nucleic Acids Res, vol.37, pp.7665-7677, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00527402
Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination, Proc. Natl. Acad. Sci. USA, vol.104, pp.19410-19415, 2007. ,
Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center, Mol. Cell, vol.11, pp.425-435, 2003. ,
Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit, J. Biol. Chem, vol.283, pp.26026-26036, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00297133
rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity, Mol. Cell, vol.28, pp.965-977, 2007. ,
Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing, RNA, vol.15, pp.1716-1728, 2009. ,
A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast, RNA, vol.9, pp.771-779, 2003. ,
rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells, Mol. Cell, vol.44, pp.660-666, 2011. ,
Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation, Wiley Interdiscip Rev. RNA, vol.2, pp.571-581, 2011. ,
Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly, EMBO J, vol.35, pp.654-667, 2016. ,
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells, Nature, vol.515, pp.143-146, 2014. ,
Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA, Cell, vol.159, pp.148-162, 2014. ,
Pseudouridine synthases, Chem. Biol, vol.13, pp.1125-1135, 2006. ,
Formation of the conserved pseudouridine at position 55 in archaeal tRNA, Nucleic Acids Res, vol.34, pp.4293-4301, 2006. ,
Crystal structure of human Pus10, a novel pseudouridine synthase, J. Mol. Biol, vol.373, pp.1243-1254, 2007. ,
The structure and function of small nucleolar ribonucleoproteins, Nucleic Acids Res, vol.35, pp.1452-1464, 2007. ,
The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA, Wiley Interdiscip Rev. RNA, vol.3, pp.397-414, 2012. ,
RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP, Genes Dev, vol.19, pp.1238-1248, 2005. ,
Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation, Nucleic Acids Res, vol.33, pp.3133-3144, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-01662780
The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs, Nat. Struct. Mol. Biol, vol.12, pp.1101-1107, 2005. ,
Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity, Nucleic Acids Res, vol.34, pp.826-839, 2006. ,
Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita, Mol. Cell, vol.21, pp.249-260, 2006. ,
Comparative study of two box H/ACA ribonucleoprotein pseudouridine-synthases: relation between conformational dynamics of the guide RNA, enzyme assembly and activity, PLoS One, vol.8, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01452159
Crystal structure of an H/ACA box ribonucleoprotein particle, Nature, vol.443, pp.302-307, 2006. ,
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA, Nat. Struct. Mol. Biol, vol.16, pp.740-746, 2009. ,
Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase, Mol. Cell, vol.34, pp.427-439, 2009. ,
RNA size is a critical factor for U-containing substrate selectivity and permanent pseudouridylated product release during the RNA:Psi-synthase reaction catalyzed by box H/ACA sRNP enzyme at high temperature, Biochimie, vol.113, pp.134-142, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01451901
Long-distance placement of substrate RNA by H/ACA proteins, RNA, vol.14, pp.2086-2094, 2008. ,
Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation, Nucleic Acids Res, vol.43, pp.7207-7216, 2015. ,
Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation, Nucleic Acids Res, vol.40, pp.10925-10936, 2012. ,
Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ ACA sRNA-guided machinery, Nucleic Acids Res, vol.37, pp.1308-1322, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00529750
Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation, RNA Biol, vol.4, pp.101-109, 2007. ,
Archaeal proteins Nop10 and Gar1 increase the catalytic activity of Cbf5 in pseudouridylating tRNA, Sci. Rep, vol.2, 2012. ,
Structure-function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation, RNA, vol.22, pp.1604-1619, 2016. ,
Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Psi55-synthase and RNA-guided RNA:Psi-synthase activities, Nucleic Acids Res, vol.35, pp.5610-5624, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-01662765
Contribution of two conserved histidines to the dual activity of archaeal RNA guide-dependent and-independent pseudouridine synthase Cbf5, RNA, vol.21, pp.1233-1239, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01451676
, Scientific RepoRts |, vol.8, 2018.
Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide, RNA, vol.17, pp.244-250, 2011. ,
Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii, RNA, vol.17, pp.1367-1380, 2011. ,
The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA, RNA, vol.18, pp.421-433, 2012. ,
Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA, RNA, vol.14, pp.2521-2527, 2008. ,
Role of forefinger and thumb loops in production of Psi54 and Psi55 in tRNAs by archaeal Pus10, RNA, vol.19, pp.1279-1294, 2013. ,
tRNA binding, positioning, and modification by the pseudouridine synthase Pus10, J. Mol. Biol, vol.425, pp.3863-3874, 2013. ,
DOI : 10.1016/j.jmb.2013.05.022
Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs, Nucleic Acids Res, vol.36, pp.2459-2475, 2008. ,
Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes, Genome Res, vol.15, pp.352-363, 2005. ,
Genetic analysis of DNA repair in the hyperthermophilic archaeon. Thermococcus kodakaraensis, Genes Genet. Syst, vol.85, pp.243-257, 2010. ,
Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis, Appl. Environ. Microbiol, vol.71, pp.3889-3899, 2005. ,
Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, J. Bacteriol, vol.185, pp.210-220, 2003. ,
On the origin of operons and their possible role in evolution toward thermophily, J. Mol. Evol, vol.49, pp.432-438, 1999. ,
Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp, KOD1. Archaea, vol.1, pp.263-267, 2004. ,
UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation, Mol. Microbiol, vol.70, pp.938-952, 2008. ,
Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage, J. Bacteriol, vol.189, pp.8708-8718, 2007. ,
Ca(2+)-dependent cell aggregation of halophilic archaeon. Halobacterium salinarum, J. Biosci. Bioeng, vol.100, pp.681-684, 2005. ,
Reconstitution of archaeal H/ACA sRNPs and test of their activity, Methods Enzymol, vol.425, pp.25016-25021, 2007. ,
Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23S RNA, Biochemistry, vol.37, pp.15951-15957, 1998. ,
Physiological analysis of the role of truB in Escherichia coli: a role for tRNA modification in extreme temperature resistance, Microbiology, vol.148, pp.3511-3520, 2002. ,
Archaeal genetics-the third way, Nat. Rev. Genet, vol.6, pp.58-73, 2005. ,
Genetic techniques for the archaea, Annu. Rev. Genet, vol.47, pp.539-561, 2013. ,
Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales, FEMS Microbiol. Rev, vol.35, pp.577-608, 2011. ,
Expanding and understanding the genetic toolbox of the hyperthermophilic genus Sulfolobus, Biochem. Soc. Trans, vol.37, pp.97-101, 2009. ,
Towards a systems approach in the genetic analysis of archaea: Accelerating mutant construction and phenotypic analysis in Haloferax volcanii, Archaea, p.426239, 2010. ,
A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes, Archaea, vol.2, pp.211-219, 2009. ,
Box C/D RNA-guided 2?-O methylations and the intron of tRNATrp are not essential for the viability of Haloferax volcanii, J. Bacteriol, vol.190, pp.7308-7313, 2008. ,
Overview of the genetic tools in the, Archaea. Front. Microbiol, vol.3, p.337, 2012. ,
Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA, Mol. Cell. Biol, vol.19, pp.7461-7472, 1999. ,
Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells, RNA, vol.6, pp.1870-1881, 2000. ,
Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus, Nucleic Acids Res, vol.39, pp.2304-2318, 2011. ,
Highly conserved modified nucleosides influence Mg 2+-dependent tRNA folding, Nucleic Acids Res, vol.30, pp.4751-4760, 2002. ,
Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990. ,
Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis, Appl. Environ. Microbiol, vol.70, pp.1277-1286, 2004. ,
, In Methods Enzymol, vol.425, pp.21-53, 2007.
Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique, Biochemistry, vol.32, pp.9754-9762, 1993. ,
Optimizing splinted ligation of highly structured small RNAs, RNA, vol.11, 1909. ,
Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography, Biochimie, vol.77, pp.142-144, 1995. ,
, Scientific RepoRts |, vol.8, 2018.
,