The box C/D sRNP dimeric architecture is conserved across domain Archaea

Bower-Phipps, Kathleen R.; Taylor, David W.; Wang, Hongwei; Baserga, Susan J.

doi:10.1261/rna.033134.112

Cited by 21 publications

(38 citation statements)

References 63 publications

(139 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nop56 and Nop58 have extensive coiled-coil domains with which they heterodimerize. Although there are both single-particle electron microscopic and crystallographic structures of complete enzymatically active archaeal box C/D s(no)RNPs (Bleichert et al 2009;Bleichert and Baserga 2010;Lin et al 2011;Bower-Phipps et al 2012), no structure yet exists for the yeast box C/D snoRNP.…”

Section: Pre-rrna Processing Can Occur Cotranscriptionallymentioning

confidence: 99%

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

2013

View full text Add to dashboard Cite

Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (.5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes. TABLE OF CONTENTS Abstract 643Introduction 644

show abstract

Section: Pre-rrna Processing Can Occur Cotranscriptionallymentioning

confidence: 99%

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

2013

View full text Add to dashboard Cite

show abstract

“…The model was derived in the absence of the substrate RNAs and the guide sRNA was not visible in the microscopy images, thus preventing any conclusion on the location of the substrates D and D ′ . Later, the same group demonstrated that all box C/D sRNPs from Archaea are di-RNPs, while a mono-RNP is obtained only when assembling the complex around an artificial two-piece guide sRNA (Bower-Phipps et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency

Graziadei

Masiewicz

Lapinaitė

et al. 2016

RNA

View full text Add to dashboard Cite

RNA modifications confer complexity to the 4-nucleotide polymer; nevertheless, their exact function is mostly unknown. rRNA 2 ′ -O-ribose methylation concentrates to ribosome functional sites and is important for ribosome biogenesis. The methyl group is transferred to rRNA by the box C/D RNPs: The rRNA sequence to be methylated is recognized by a complementary sequence on the guide RNA, which is part of the enzyme. In contrast to their eukaryotic homologs, archaeal box C/D enzymes can be assembled in vitro and are used to study the mechanism of 2 ′ -O-ribose methylation. In Archaea, each guide RNA directs methylation to two distinct rRNA sequences, posing the question whether this dual architecture of the enzyme has a regulatory role. Here we use methylation assays and low-resolution structural analysis with small-angle X-ray scattering to study the methylation reaction guided by the sR26 guide RNA from Pyrococcus furiosus. We find that the methylation efficacy at sites D and D ′ differ substantially, with substrate D ′ turning over more efficiently than substrate D. This observation correlates well with structural data: The scattering profile of the box C/D RNP half-loaded with substrate D ′ is similar to that of the holo complex, which has the highest activity. Unexpectedly, the guide RNA secondary structure is not responsible for the functional difference at the D and D ′ sites. Instead, this difference is recapitulated by the nature of the first base pair of the guide-substrate duplex. We suggest that substrate turnover may occur through a zip mechanism that initiates at the 5 ′ -end of the product.

show abstract

“…This mechanism is incompatible with the RNA-swapped model for dimeric C/D RNP. C/D RNA has proposed to be swapped between two different protein complexes in the di-RNP (34)(35)(36)(37)(38), rather than associating with the same Nop5 dimer as shown in the mono-RNP structure (30). It also has been argued that the RNA-swapped di-RNP model is advantageous for accommodating long guide-substrate duplexes compared with the mono-RNP model.…”

Section: Significancementioning

confidence: 99%

Box C/D guide RNAs recognize a maximum of 10 nt of substrates

Yang

Lin

2016

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

View full text Add to dashboard Cite

Box C/D RNAs guide site-specific 2′-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D′ and boxes C′ to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C′ side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNAswapped model for dimeric C/D RNP.B ox C/D RNAs are a large family of noncoding RNAs conserved in archaea and eukaryotes (1-3). The majority of these RNAs function as guides in site-specific 2′-O-methylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (4-7). A few special members, including U3 and U14, small nucleolar RNAs are required for pre-rRNA processing and ribosome assembly. One of the most abundant modifications in rRNAs, 2′-O-methylated nucleotides cluster in functionally important regions and are believed to fine-tune ribosome structure and function (8)(9)(10)(11).Box C/D RNAs have a bipartite structure and contain the C (RUGAUGA; R is a purine) and D (CUGA) box motifs at two ends and the related C′ and D′ box motifs in the internal regions. Each pair of boxes C and D combine into a characteristic kink turn (K-turn) or K-loop structure (12-15). The spacer regions located between boxes D and C′ (D spacer) and between boxes D′ and C (D′ spacer) harbor the guide sequence. The guide sequence can potentially form 10-21 bp with complementary sequences in substrate RNAs and select the fifth nucleotide apart from box D′/D for modification (5).To form a functional ribonucleoprotein (RNP) enzyme, each C/D RNA associates with four core proteins [Snu13, fibrillarin (Nop1 in yeast), Nop56, and Nop58] in eukaryotes (16-23) and with three proteins (L7Ae, fibrillarin, and Nop5) in archaea (24). The homologous eukaryotic Nop56 and Nop58 proteins are replaced by a single protein, Nop5, in archaea. Fibrillarin is the catalyst that transfers a methyl group from S-adenosylmethionine to the target ribose (21, 25). The RNA-guided methylation activity has been reconstituted for archaeal C/D RNPs (24), but not yet for eukaryotic complexes (26).Structural st...

show abstract

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Cited by 21 publications

References 63 publications

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency

Box C/D guide RNAs recognize a maximum of 10 nt of substrates

Contact Info

Product

Resources

About