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

Manival, Xavier; Charron, Christophe; Fourmann, Jean-Baptiste; Godard, François; Charpentier, Bruno; Branlant, Christiane

doi:10.1093/nar/gkj482

Cited by 69 publications

(115 citation statements)

References 49 publications

Supporting

Mentioning

110

Contrasting

Order By: Relevance

“…To address this question, a great deal of efforts have been expended to solve the crystal structures of archaeal box H/ACA snRNP complexes. As a result, the structures of various forms, from the initial complex of three core proteins to a complete, substrate-bound box H/ACA RNP, have been solved (Li and Ye, 2006;Manival et al, 2006;Rashid et al, 2006;Liang et al, 2007;Duan et al, 2009;Liang et al, 2009). A detailed picture of how this most complex pseudouridylase modifies its substrate has now become available.…”

Section: Spliceosomal Snrna Pseudouridylation Is Induced At Novel Sitmentioning

confidence: 99%

Pseudouridines in spliceosomal snRNAs

2011

Protein Cell

View full text Add to dashboard Cite

Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing. All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription. Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing. Many of these modified nucleotides are conserved across species lines. Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms: an RNA-dependent mechanism and an RNA-independent mechanism. The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied. Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important. Besides the currently known pseudouridines (constitutive modifications), recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions, thus strongly suggesting that pseudouridylation is also a regulatory modification.

show abstract

Section: Spliceosomal Snrna Pseudouridylation Is Induced At Novel Sitmentioning

confidence: 99%

Pseudouridines in spliceosomal snRNAs

2011

Protein Cell

View full text Add to dashboard Cite

show abstract

“…The structure of the archaeal pseudouridylase Cbf5 was solved complexed with Nop10 [5,6] or with Nop10 and Gar1 [4]. Based on structural and sequence homologies, pseudouridylases are classified into 5 families, RluA, RsuA, TruA, TruB, and TruD [10].…”

Section: The Structuresmentioning

confidence: 99%

“…Recently, three groups solved the crystal structures of archaeal H/ACA RNP core complexes consisting of two or three core proteins (Fig. 1) [4][5][6]. For the first time, these structures provide molecular details of protein-protein interactions in the H/ACA core complex and of the pseudouridylase itself.…”

Section: Introductionmentioning

confidence: 99%

“…Although Nop10 alone appears to be an intrinsically disordered protein [13], it becomes structured upon Cbf5 binding. This tight interaction with Cbf5 may be important to freeze the catalytic domain in the most favorable position for catalysis and to extend the positive surface potential of Cbf5 for H/ACA and substrate RNA binding [4][5][6]. In fact, Nop10 and its C-terminal alpha helix alone promote binding of substrate RNA in gel shift assays and are sufficient for reconstituting RNA-guided pseudouridylase activity in the context of Cbf5 and L7Ae [6].…”

mentioning

confidence: 99%

See 1 more Smart Citation

How a single protein complex accommodates many different H/ACA RNAs

Meier

2006

Trends in Biochemical Sciences

View full text Add to dashboard Cite

Over 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins. The function of these H/ACA RNPs is essential for ribosome biogenesis, pre-mRNA splicing, telomere maintenance, and, likely, for additional cellular processes. Recent crystal structures of archaeal H/ACA protein complexes illustrate how the same four proteins accommodate more than 100 distinct though related H/ACA RNAs and reveal a spatial mutation cluster underlying the bone marrow failure syndrome dyskeratosis congenita (DC).Keywords H/ACA RNPs; H/ACA RNAs; crystal structure; core proteins; dyskeratosis congenita; RNAprotein interaction The vast majority of mammalian H/ACA RNPs engage in isomerization of uridines to pseudouridines (pseudouridylation) in ribosomal and spliceosomal small nuclear RNAs. Although the function of most pseudouridines is unknown, some are essential for optimal translation and for pre-mRNA splicing [1]. Perhaps the most intriguing species of H/ACA RNPs are defined by the snoRNA U17/E1 (snR30 in yeast), telomerase RNA (which ends in an H/ACA RNA structure), and a growing number of orphan H/ACA RNAs (without complementarity to any stable RNAs) [2]. U17 is the only essential H/ACA RNA and is required for pre-ribosomal RNA processing; telomerase RNA is required for the replication of chromosome ends; and the orphan H/ACA RNAs are by definition of unknown function but potentially involved in similar important processes as U17 and telomerase RNA (Fig. 1) [3]. Recently, three groups solved the crystal structures of archaeal H/ACA RNP core complexes consisting of two or three core proteins (Fig. 1) [4][5][6]. For the first time, these structures provide molecular details of protein-protein interactions in the H/ACA core complex and of the pseudouridylase itself. meier@aecom.yu Fig. 1), the other class being C/D RNAs. On average 130-140 nucleotides in length, H/ACA RNAs conform to a consensus 5'-hairpin-hinge-hairpin-tail-3' secondary structure with the characteristic ACA trinucleotide exactly three residues from the 3' end ( Fig. 1). H/ACA RNAs identify the ~130 known mammalian pseudouridylation sites by base pairing to a few nucleotides flanking the target uridines. Complementarity to target RNAs lies in the upper half of a bulge (pseudouridylation pocket) of one or both of the hairpins placing the unpaired target uridine at the bottom of a helix [7,8]. Pseudouridylation is catalyzed by one of the four H/ACA core proteins, the pseudouridylase NAP57 (also dyskerin or, in yeast and archaea, Cbf5) [9]. The small basic proteins GAR1, NOP10, and NHP2 (L7Ae in archaea) round out H/ACA RNPs. All four core proteins, except GAR1, are essential for the structural integrity of H/ACA RNPs [3]. The structuresThe structure of the archaeal pseudouridylase Cbf5 was solved complexed with Nop10 [5,6] or with Nop10 and Gar1 [4]. Based on structural and sequence homologies, pseudouridylases are classified into 5 families, RluA, RsuA, TruA, TruB, and TruD [10].Crystal structur...

show abstract

“…Conversely, the exchange of the other core proteins could reflect a possible rearrangement or breathing of the complex during catalysis. For example, recent crystal structures of partial archaeal H/ACA protein complexes demonstrate how NOP10 brackets the catalytic domain of NAP57 (Hamma et al 2005;Manival et al 2006;Rashid et al 2006). During catalysis this NOP10-NAP57 interaction may need to be loosened to allow access to and/or release of substrate RNAs.…”

Section: Protein Dynamics Of H/aca Rnpsmentioning

confidence: 99%

Dynamic association and localization of human H/ACA RNP proteins

Kittur¹,

Darzacq²,

Roy³

et al. 2006

RNA

View full text Add to dashboard Cite

Mammalian H/ACA RNPs are essential for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. To form mature RNA-protein complexes, one H/ACA RNA associates with four core proteins. In the cell, this process is assisted by at least one nuclear assembly factor, NAF1. Here we report several unanticipated dynamic aspects of H/ACA RNP proteins. First, when overexpressed, NAF1 delocalizes to the cytoplasm. However, its nucleocytoplasmic shuttling properties remain unaffected. These observations demonstrate a subtle equilibrium between NAF1 expression levels and the availability of NAF1 nuclear binding sites. Second, although NAF1 is excluded from mature RNPs in nucleoli and Cajal bodies, NAF1 associates with mature H/ACA RNA in cell lysates. This association occurs post-lysis because it is observed even when NAF1 and the H/ACA RNA are expressed in separate cells. This documents a protein-RNP association in cell lysates that is absent from intact cells. Third, in similar experiments, all H/ACA core proteins, except NAP57, exchange with their exogenous counterparts, portraying an unexpected dynamic picture of H/ACA RNPs. Finally, the irreversible association of only NAP57 with H/ACA RNA and the conundrum that only NAP57 is mutated in X-linked dyskeratosis congenita (even though most core proteins are required for maintaining H/ACA RNAs) may be more than a coincidence.

show abstract

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

Cited by 69 publications

References 49 publications

Pseudouridines in spliceosomal snRNAs

Pseudouridines in spliceosomal snRNAs

How a single protein complex accommodates many different H/ACA RNAs

Dynamic association and localization of human H/ACA RNP proteins

Contact Info

Product

Resources

About