ATP-dependent unwinding of U4/U6 snRNAs by the Brr2 helicase requires the C terminus of Prp8

Maeder, Corina; Kutach, Alan K.; Guthrie, Christine

doi:10.1038/nsmb.1535

Cited by 116 publications

(169 citation statements)

References 58 publications

Supporting

Mentioning

162

Contrasting

Order By: Relevance

“…It is interesting to compare these findings with two recent studies performed in yeast (Boon, et al, 2007;Maeder, et al, 2009). Both studies showed that the mutations which cause RP in human patients, when present in yeast Prp8 protein, result in its reduced association with the DEAD-box helicase Brr2p in the yeast nucleus (Boon, et al, 2007;Maeder, et al, 2009).…”

Section: Discussionmentioning

confidence: 74%

“…Both studies showed that the mutations which cause RP in human patients, when present in yeast Prp8 protein, result in its reduced association with the DEAD-box helicase Brr2p in the yeast nucleus (Boon, et al, 2007;Maeder, et al, 2009). The association of Prp8p with Brr2p is thought to be essential for the production of a mature spliceosome and yeast carrying the RP-causing mutations have reduced splicing activity.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Prognosis for splicing factor PRPF8 retinitis pigmentosa, novel mutations and correlation between human and yeast phenotypes

et al. 2010

View full text Add to dashboard Cite

PRPF8-retinitis pigmentosa is said to be severe but there has been no overview of phenotype across different mutations. We screened RP patients for PRPF8 mutations and identified three new missense mutations, including the first documented mutation outside exon 42 and the first de novo mutation. This brings the known RP-causing mutations in PRPF8 to nineteen. We then collated clinical data from new and published cases to determine an accurate prognosis for PRPF8-RP. Clinical data for 75 PRPF8-RP patients were compared, revealing that while the effect on peripheral retinal function is severe, patients generally retain good visual acuity in at least one eye until the fifth or sixth decade. We also noted that prognosis for PRPF8-RP differs with different mutations, with p.H2309P or p.H2309R having a worse prognosis than p.R2310K. This correlates with the observed difference in growth defect severity in yeast lines carrying the equivalent mutations, though such correlation remains tentative given the limited number of mutations for which information is available. The yeast phenotype is caused by lack of mature spliceosomes in the nucleus, leading to reduced RNA splicing function. Correlation between yeast and human phenotypes suggests that splicing factor RP may also result from an underlying splicing deficit.

show abstract

Section: Discussionmentioning

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Prognosis for splicing factor PRPF8 retinitis pigmentosa, novel mutations and correlation between human and yeast phenotypes

et al. 2010

View full text Add to dashboard Cite

show abstract

“…Of the 25 DEAD-box proteins in Saccharomyces cerevisiae, five (eIF4A, Fal1, Ded1, Dbp5, and Dbp8) are known to be regulated by cofactors (12,19,21,28,34,35,(65)(66)(67). Similarly, three related SF2-helicases from the DEAH and Ski2-like subfamilies (Prp43, Mtr4, and Brr2) are also regulated by cofactors (22,23,25,(68)(69)(70)(71). These cofactors can increase or decrease the rates of ATP hydrolysis, RNA unwinding, or phosphate or RNA release.…”

Section: Discussionmentioning

confidence: 99%

Cofactor-dependent specificity of a DEAD-box protein

Young

Khoshnevis

Karbstein

2013

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

View full text Add to dashboard Cite

DEAD-box proteins, a large class of RNA-dependent ATPases, regulate all aspects of gene expression and RNA metabolism. They can facilitate dissociation of RNA duplexes and remodeling of RNA-protein complexes, serve as ATP-dependent RNA-binding proteins, or even anneal duplexes. These proteins have highly conserved sequence elements that are contained within two RecA-like domains; consequently, their structures are nearly identical. Furthermore, crystal structures of DEAD-box proteins with bound RNA reveal interactions exclusively between the protein and the RNA backbone. Together, these findings suggest that DEAD-box proteins interact with their substrates in a nonspecific manner, which is confirmed in biochemical experiments. Nevertheless, this contrasts with the need to target these enzymes to specific substrates in vivo. Using the DEAD-box protein Rok1 and its cofactor Rrp5, which both function during maturation of the small ribosomal subunit, we show here that Rrp5 provides specificity to the otherwise nonspecific biochemical activities of the Rok1 DEAD-domain. This finding could reconcile the need for specific substrate binding of some DEAD-box proteins with their nonspecific binding surface and expands the potential roles of cofactors to specificity factors. Identification of helicase cofactors and their RNA substrates could therefore help define the undescribed roles of the 19 DEAD-box proteins that function in ribosome assembly.RNA helicases | annealing D EAD-box proteins are RNA-binding ATPases that are involved in all aspects of RNA metabolism: translation initiation, pre-mRNA splicing, mRNA export and decay, and ribosome biogenesis. In these processes, their functions include RNA duplex unwinding, RNA-protein complex remodeling, RNA duplex annealing, and ATP-dependent RNA binding (1-5).In vivo, these enzymes have specific functions that often involve the recognition of specific RNAs and the discrimination against a myriad of nonsubstrates. Nevertheless, only DbpA, a DEAD-box protein involved in bacterial ribosome assembly (6-8), has sequence-specific ATPase activity (6, 9), which arises from unique sequences in its C terminus (10). Such sequence specificity has not been demonstrated for any other DEAD-box protein and is consistent with their highly conserved structures and the almost universal conservation of residues that contact the RNA. Furthermore, analysis of the structures of RNA-bound DEAD-box proteins reveals that RNA contacts are made with the sugarphosphate backbone (11-17), largely precluding sequence-specific interactions between DEAD-box proteins and RNA.Many DEAD-box and related DEAH-box proteins function in conjunction with cofactors (ref. 18 and references therein). These cofactors can regulate the activity of DEAD-box or DEAH-box proteins by stimulating or inhibiting their ATPase, helicase, RNAbinding, or nucleotide-binding activities. Interestingly, cofactors are often RNA-binding proteins (19)(20)(21)(22)(23)(24)(25). We and others therefore postulated that these cofactors could als...

show abstract

“…On the other hand, isolated Brr2 is a comparatively weak helicase, 25,40,41 and its U4/U6 di-snRNA substrate is stabilized by extensive base pairing and bound proteins, [12][13][14]29,42,43 suggesting that the helicase may also depend on specific activation to efficiently unwind the U4/U6 duplex at the right time.…”

Section: Brr2 Requires Tight Regulationmentioning

confidence: 99%

“…This idea is in line with previous proposals of Brr2 functioning as a landing pad for multiple other helicases, which might sequentially interact in similar fashion with the C-terminal cassette. 40,41,52,63,64 Based on the observations that a temperature-sensitive yeast Brr2 variant (E909K), encoded by the slt22-1 allele, is synthetically lethal with mutations in U2 or U6 snRNAs that affect the stability or conformation of U2/U6 helix II, and that the ATPase activity of this variant is no longer stimulated by a U2/ U6 duplex, it was proposed that Brr2 might proofread U2/U6 interactions. 45 Furthermore, different cross-linking profiles of wt Brr2 and a variant exhibiting a residue exchange (G858R) in the NC 5 0 HP/separator loop with U6 snRNA 46 together with the latter variant exhibiting a second step defect and showing synthetic lethality with step 2 mutations in Slu7, Prp18 and Prp16 46,49 suggest that Brr2 participates in a transient opening of the catalytic core between the 2 steps of splicing, which is characterized by the intermittent disruption of U6-5SS and U2-U6 interactions.…”

Section: Brr2 Regulation During Splicingmentioning

confidence: 99%

Functions and regulation of the Brr2 RNA helicase during splicing

2016

View full text Add to dashboard Cite

Pre-mRNA splicing entails the stepwise assembly of an inactive spliceosome, its catalytic activation, splicing catalysis and spliceosome disassembly. Transitions in this reaction cycle are accompanied by compositional and conformational rearrangements of the underlying RNA-protein interaction networks, which are driven and controlled by 8 conserved superfamily 2 RNA helicases. The Ski2-like helicase, Brr2, provides the key remodeling activity during spliceosome activation and is additionally implicated in the catalytic and disassembly phases of splicing, indicating that Brr2 needs to be tightly regulated during splicing. Recent structural and functional analyses have begun to unravel how Brr2 regulation is established via multiple layers of intra-and inter-molecular mechanisms. Brr2 has an unusual structure, including a long N-terminal region and a catalytically inactive C-terminal helicase cassette, which can auto-inhibit and auto-activate the enzyme, respectively. Both elements are essential, also serve as protein-protein interaction devices and the N-terminal region is required for stable Brr2 association with the tri-snRNP, tri-snRNP stability and retention of U5 and U6 snRNAs during spliceosome activation in vivo. Furthermore, a C-terminal region of the Prp8 protein, comprising consecutive RNase H-like and Jab1/MPN-like domains, can both up-and downregulate Brr2 activity. Biochemical studies revealed an intricate cross-talk among the various cis-and transregulatory mechanisms. Comparison of isolated Brr2 to electron cryo-microscopic structures of yeast and human U4/U6 U5 tri-snRNPs and spliceosomes indicates how some of the regulatory elements exert their functions during splicing. The various modulatory mechanisms acting on Brr2 might be exploited to enhance splicing fidelity and to regulate alternative splicing. KEYWORDSPre-mRNA splicing; regulation of pre-mRNA splicing; remodeling of RNAprotein complexes; RNA helicase structure, function and regulation; spliceosome catalytic activation

show abstract

ATP-dependent unwinding of U4/U6 snRNAs by the Brr2 helicase requires the C terminus of Prp8

Cited by 116 publications

References 58 publications

Prognosis for splicing factor PRPF8 retinitis pigmentosa, novel mutations and correlation between human and yeast phenotypes

Prognosis for splicing factor PRPF8 retinitis pigmentosa, novel mutations and correlation between human and yeast phenotypes

Cofactor-dependent specificity of a DEAD-box protein

Functions and regulation of the Brr2 RNA helicase during splicing

Contact Info

Product

Resources

About