The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs

Winkler, William E.; Grundy, Frank J.; Murphy, Brooke A.; Henkin, Tina M.

doi:10.1017/s1355838201002370

Cited by 109 publications

(137 citation statements)

References 20 publications

Supporting

Mentioning

130

Contrasting

Order By: Relevance

“…A K-turn motif located in the P2 stem has been shown to be important for the structure and activity of the riboswitch. 45,46 The K-turn has been originally observed in the 23 rRNA and is characterized by the presence of a sharp bend in the phosphate backbone, which is important to mediate RNA tertiary structure interactions and protein…”

Section: Structure and Activity Of The Sam-i Riboswitchmentioning

confidence: 99%

Folding of the SAM-I riboswitch

et al. 2012

View full text Add to dashboard Cite

Section: Structure and Activity Of The Sam-i Riboswitchmentioning

confidence: 99%

Folding of the SAM-I riboswitch

et al. 2012

View full text Add to dashboard Cite

“…The K-turn was first identified as a novel motif occurring multiple times in the ribosome. Further examples have been found in mRNA (Mao et al 1999;Winkler et al 2001;Allmang et al 2002;Montange and Batey 2006), guide RNAs (Kuhn et al 2002;Watkins et al 2002;Bortolin et al 2003;MarmierGourrier et al 2003;Rozhdestvensky et al 2003), and spliceosomal RNA (Vidovic et al 2000;Watkins et al 2000).…”

Section: Introductionmentioning

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

View full text Add to dashboard Cite

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.

show abstract

“…The motif has been described either as the ''kink-turn,'' because of the sharp bend present in the phosphodiester backbone of the RNA axis, or as the ''GA motif,'' based on the presence of the highly conserved GA dinucleotide in the asymmetric internal loop (21,22). The motif is a highly conserved feature of the 5Ј stem loop of U4 snRNA, is generated by the C and D box (or CЈ and DЈ) sequences of C͞D box snoRNAs, and is present in other RNAs from both eukaryotes and prokaryotes (21,22).Archaea are prokaryotic organisms, distinct from Bacteria and believed to be related to the earliest eukaryotes (23). By employing biochemical and computational methods, the presence of up to 50 or more distinct C͞D box small RNAs (sRNAs) was demonstrated in several species of hyperthermophilic .…”

mentioning

confidence: 99%

“…The fold is generally characterized by two tandem G⅐A base pairs, a high degree of purine stacking, and a single base rotated out of the RNA loop that inserts into a pocket of the protein (20). The motif has been described either as the ''kink-turn,'' because of the sharp bend present in the phosphodiester backbone of the RNA axis, or as the ''GA motif,'' based on the presence of the highly conserved GA dinucleotide in the asymmetric internal loop (21,22). The motif is a highly conserved feature of the 5Ј stem loop of U4 snRNA, is generated by the C and D box (or CЈ and DЈ) sequences of C͞D box snoRNAs, and is present in other RNAs from both eukaryotes and prokaryotes (21,22).…”

mentioning

confidence: 99%

In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex

Omer

Ziesche²,

Ebhardt³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

177

223

View full text Add to dashboard Cite

The genomes of hyperthermophilic Archaea encode dozens of methylation guide, C͞D box small RNAs that guide 2 -O-methylation of ribose to specific sites in rRNA and various tRNAs. The genes encoding the Sulfolobus homologues of eukaryotic proteins that are known to be present in C͞D box small nucleolar ribonucleoprotein (snoRNP) complexes were cloned, and the proteins (aFIB, aNOP56, and aL7a) were expressed and purified. The purified proteins along with an in vitro transcript of the Sulfolobus sR1 small RNA were reconstituted in vitro, into an RNP complex. The order of assembly of the three proteins onto the RNA was aL7a, aNOP56, and aFIB. The complex was active in targeting S-adenosyl methionine (SAM)-dependent, site-specific 2 -O-methylation of ribose to a short fragment of ribosomal RNA (rRNA) that was complementary to the D box guide region of the sR1 small RNA. The presence of aFIB was essential for methylation; mutant proteins having amino acid replacements in the SAM-binding motif of aFIB were able to assemble into an RNP complex, but the resulting complexes were defective in methylation activity. These experiments define the minimal number of components and the conditions required to achieve in vitro RNA guide-directed 2 -O-methylation of ribose in a target RNA.T he eukaryotic nucleolus is a highly specialized organelle where rRNA is transcribed, processed, folded, and assembled along with ribosomal proteins into small and large ribosomal subunits (1-5). During this process, up to a hundred or more nucleotide modifications are introduced into the ribosomal RNA (rRNA) by two distinct families of small nucleolar ribonucleoprotein (snoRNP) complexes. The snoRNAs in these RNP complexes contain short antisense guide elements that are used to target modifications to specific locations within the rRNAs. One guide family, the C͞D box snoRNPs, targets site-specific 2Ј-O-methylation of ribose (6-9), and the other guide family, the H͞ACA snoRNPs, targets site-specific conversion of uridine to pseudouridine (10).The C͞D box snoRNAs are characterized by a bipartite structure with conserved C box (RUGAUGA) and D box (CUGA) motifs near their respective 5Ј and 3Ј ends and related CЈ (UGAUGA) and DЈ (CUGA) motifs near the center of the molecule. The antisense elements are located upstream of the D or DЈ motifs and are generally 10 or more nucleotides (nt) in length. Methylation is directed to the rRNA nucleotide that participates in a Watson-Crick base pair five nucleotides upstream from the start of the D or DЈ box; this is the N plus five rule (10-12). Although the general mechanism used by these RNP complexes in mediating modification has been deduced from in vivo biochemical and genetic observations, isolation and characterization of the structure and the in vitro activity of these guide complexes have not been described.The human C͞D box snoRNAs associate with several essential proteins, including fibrillarin, NOP56, and NOP58 (paralogous proteins derived from a gene duplication event), and a 15.5-kDa protein (8,(12)...

show abstract

The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs

Cited by 109 publications

References 20 publications

Folding of the SAM-I riboswitch

Folding of the SAM-I riboswitch

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

In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex

Contact Info

Product

Resources

About