Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein

Szewczak, Lara; Gabrielsen, J. Scott; DeGregorio, Suzanne J.; Strobel, Scott A.; Steitz, Joan A.

doi:10.1261/rna.2830905

Cited by 50 publications

(62 citation statements)

References 42 publications

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“…Similar patterns of L7Ae binding and methylation activity were also observed with the sR1 guide RNA of Sulfolobus acidocaldarius and its circular permuted version that was prepared like our CpIntron (Omer et al 2006). Even in the eukaryal system, preferential binding of the human 15.5K protein to the terminal box C/D of the Xenopus U25 snoRNA was not changed by circularly permuting the RNA (Szewczak et al 2005). The similarity between pre-tRNA Trp intron and its circularly permuted version was not unexpected, since the intron is normally spliced out as circular RNA and can be detected inside the cells (Salgia et al 2003), and both linear and circular versions of this intron can guide 29-O-methylation (Singh et al 2004).…”

Section: L7ae Induced Structural Rearrangements In Srnassupporting

confidence: 67%

“…Sometimes the K-turn associated with box C9/D9 is modified to the K-loop (Nolivos et al 2005). Both L7Ae and 15.5K proteins recognize the K-turn motif, but only L7Ae can recognize the K-loop (Charron et al 2004;Hamma and Ferre-D'Amare 2004;Moore et al 2004;Cojocaru et al 2005;Nolivos et al 2005;Suryadi et al 2005;Szewczak et al 2005;Turner et al 2005). Binding of L7Ae to the K-turn changes the conformation of the box C/D motif, and this altered RNA conformation is then recognized by aNop5p (Rashid et al 2003).…”

Section: Introductionmentioning

confidence: 99%

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Dynamic guide–target interactions contribute to sequential 2′-O-methylation by a unique archaeal dual guide box C/D sRNP

Singh

Gurha²,

Gupta³

2008

RNA

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Assembly and guide-target interaction of an archaeal box C/D-guide sRNP was investigated under various conditions by analyzing the lead (II)-induced cleavage of the guide RNA. Guide and target RNAs derived from Haloferax volcanii pre-tRNA Trp were used with recombinant Methanocaldococcus jannaschii core proteins in the reactions. Core protein L7Ae binds differentially to C/D and C9/D9 motifs of the guide RNA, and interchanging the two motifs relative to the termini of the guide RNA did not affect L7Ae binding or sRNA function. L7Ae binding to the guide RNA exposes its D9-guide sequence first followed by the D guide. These exposures are reduced when aNop5p and aFib proteins are added. The exposed guide sequences did not pair with the target sequences in the presence of L7Ae alone. The D-guide sequence could pair with the target in the presence of L7Ae and aNop5p, suggesting a role of aNop5p in target recruitment and rearrangement of sRNA structure. aFib binding further stabilizes this pairing. After box C/D-guided modification, target-guide pairing at the D-guide sequence is disrupted, suggesting that each round of methylation may require some conformational change or reassembly of the RNP. Asymmetric RNPs containing only one L7Ae at either of the two box motifs can be assembled, but a functional RNP requires L7Ae at the box C/D motif. This arrangement resembles the asymmetric eukaryal snoRNP. Observations of initial D-guidetarget pairing and the functional requirement for L7Ae at the box C/D motif are consistent with our previous report of the sequential 29-O-methylations of the target RNA.

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Section: L7ae Induced Structural Rearrangements In Srnassupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Dynamic guide–target interactions contribute to sequential 2′-O-methylation by a unique archaeal dual guide box C/D sRNP

Singh

Gurha²,

Gupta³

2008

RNA

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“…The nearinvariant nature of this interaction is in excellent agreement with our experimental observation that folding is totally prevented by removal of the L1 29-OH in Kt-7. Interestingly, removal of the L1 29-OH has been found to be the most deleterious change for the binding of the human 15.5-kDa protein to box C/D U25 RNA in NAIM experiments (Szewczak et al 2005). …”

Section: L1 29-oh To 1n Adenine N1mentioning

confidence: 99%

The role of specific 2′-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

Liu

Lilley²

2006

RNA

137

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The role of 29-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (K-turn) has been investigated. Individual 29-OH groups have been removed by chemical synthesis, and the kinking of the RNA has been studied by gel electrophoresis and fluorescence resonance energy transfer. The results have been analyzed by reference to a database of 11 different crystallographic structures of K-turns. The potential hydrogen bonds fall into several classes. The most important are those in the core of the turn and ribose-phosphate interactions around the bulge. Of these the single most important hydrogen bond is one donated from the 29-OH of the 59 nucleotide of the bulge to the N1 of the adenine of the kink-proximal A d G pair. This is present in all known K-turn structures, and removal of the 29-OH completely prevents metal ion-induced folding. Hydrogen bonds formed in the minor grooves of the helical stems are less important, and removal of the participating 29-OH groups leads to reduced impairment of folding. These interactions are generally more polymorphic, and hydrogen bonds probably form where possible, as permitted by the global structure.

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“…Further examples have been found in mRNA (Mao et al 1999;Winkler et al 2001;Allmang et al 2002;White et al 2004) and in riboswitches (Montange and Batey 2006;Blouin and Lafontaine 2007;Heppell and Lafontaine 2008). They are very commonly found in C/D and H/ACA guide snoRNAs and in U3 snoRNA species (Kuhn et al 2002;Watkins et al 2002;Bortolin et al 2003;Marmier-Gourrier et al 2003;Rozhdestvensky et al 2003;Hamma and Ferré-D'Amaré 2004;Moore et al 2004;Szewczak et al 2005;Youssef et al 2007). There is also a near-canonical k-turn in a stem-loop of the human U4 snRNA (Vidovic et al 2000;Wozniak et al 2005).…”

Section: The Occurrence Of K-turns In Rnamentioning

confidence: 99%

A structural database for k-turn motifs in RNA

Schroeder¹,

McPhee²,

Ouellet³

et al. 2010

RNA

108

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The kink-turn (k-turn) is a common structural motif in RNA that introduces a tight kink into the helical axis. k-turns play an important architectural role in RNA structures and serve as binding sites for a number of proteins. We have created a database of known and postulated k-turn sequences and three-dimensional (3D) structures, available via the internet. This site provides (1) a database of sequence and structure, as a resource for the RNA community, and (2) a tool to enable the manipulation and comparison of 3D structures where known.

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Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein

Cited by 50 publications

References 42 publications

Dynamic guide–target interactions contribute to sequential 2′-O-methylation by a unique archaeal dual guide box C/D sRNP

Dynamic guide–target interactions contribute to sequential 2′-O-methylation by a unique archaeal dual guide box C/D sRNP

The role of specific 2′-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

A structural database for k-turn motifs in RNA

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