Published online 16 November 2005
Article |
The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn
Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, UMR 5100 Université Paul Sabatier 118 route de Narbonne, 31062 Toulouse cedex 9, France
*To whom correspondence should be addressed. Tel: +33561335975; Fax: +33561335886; Email: clouet{at}ibcg.biotoul.fr
Received September 26, 2005. Revised October 29, 2005. Accepted October 29, 2005.
The C/D guide RNAs predicted from the genomic sequences of three species of Pyrococcus delineate a family of small non-coding archaeal RNAs involved in the methylation of rRNA and tRNA. The C/D guides assemble into ribonucleoprotein (RNP) that contains the methyltransferase. The protein L7Ae, a key structural component of the RNP, binds to a Kink-turn (K-turn) formed by the C/D motif. The K-turn is a structure that consists of two RNA stems separated by a short asymmetric loop with a characteristic sharp bend (kink) between the two stems. The majority of the pyrococcal C/D guides contain a short 3 nt-spacer between the C'/D' motifs. We show here that conserved terminal stem–loops formed by the C'/D' motif of the Pyrococcus C/D RNAs are also L7Ae-binding sites. These stem–loops are related to the K-turn by sequence and structure, but they consist of a single stem closed by a terminal loop. We have named this structure the K-loop. We show that conserved non-canonical base pairs in the stem of the K-loop are necessary for L7Ae binding. For the C/D guides with a 3 nt-spacer we show that the sequence and length is also important. The K-loop could improve the stability of the C/D guide RNAs in Pyrococcal species, which are extreme hyperthermophiles.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. K. Singh, P. Gurha, and R. Gupta Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP RNA, July 1, 2008; 14(7): 1411 - 1423. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. A. Youssef, R. M. Terns, and M. P. Terns Dynamic interactions within sub-complexes of the H/ACA pseudouridylation guide RNP Nucleic Acids Res., September 25, 2007; 35(18): 6196 - 6206. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. Appel and E. S. Maxwell Structural features of the guide:target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2'-O-methylation RNA, June 1, 2007; 13(6): 899 - 911. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Clery, V. Bourguignon-Igel, C. Allmang, A. Krol, and C. Branlant An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery Nucleic Acids Res., March 19, 2007; 35(6): 1868 - 1884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. L. Reichow, T. Hamma, A. R. Ferre-D'Amare, and G. Varani The structure and function of small nucleolar ribonucleoproteins Nucleic Acids Res., March 12, 2007; 35(5): 1452 - 1464. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Clery, V. Senty-Segault, F. Leclerc, H. A. Raue, and C. Branlant Analysis of Sequence and Structural Features That Identify the B/C Motif of U3 Small Nucleolar RNA as the Recognition Site for the Snu13p-Rrp9p Protein Pair Mol. Cell. Biol., February 15, 2007; 27(4): 1191 - 1206. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. W. Hardin and R. T. Batey The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity Nucleic Acids Res., October 6, 2006; 34(18): 5039 - 5051. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Rosenblad, M. D. Lopez, P. Piccinelli, and T. Samuelsson Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes Nucleic Acids Res., October 6, 2006; 34(18): 5145 - 5156. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Omer, M. Zago, A. Chang, and P. P. Dennis Probing the structure and function of an archaeal C/D-box methylation guide sRNA RNA, September 1, 2006; 12(9): 1708 - 1720. [Abstract] [Full Text] [PDF]
|
|