Specific Alterations of U1-C Protein or U1 Small Nuclear RNA Can Eliminate the Requirement of Prp28p, an Essential DEAD Box Splicing Factor

Chen, Jeff Yi Fu; Stands, Leah; Staley, Jonathan P.; Jackups, Ronald; Latus, Lori J.; Chang, Tien Hsien

doi:10.1016/s1097-2765(01)00170-8

Cited by 191 publications

(200 citation statements)

References 43 publications

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“…Their highly localized unwindin g mode prevents large-scale unravelling of carefully assembled RNA or RNP structures, and the efficient unwinding of short duplexes is adapted to the separation of duplexes in physiological RNAs and RNPs, which rarely exceed one helical turn. Typical examples of local unwinding are thought to occur during processes that involve guide RNAs (gRNAs), such as the unwinding of small nuclear RNA (snRNA) in pre-mRNA splicing, small nucleola r RNA (snoRNA) in ribosome biogenesis or gRNA in mitochondria l RNA editing [35][36][37][38] .…”

Section: Mitochondrial Rna Editingmentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

983

1,069

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Nearly all aspects of RNA metabolism, from transcription and translation to mRNA decay, involve RNA helicases, which are enzymes that use ATP to bind or remodel RNA and RNA-protein complexes (ribonucleoprotein (RNP) complexes) 1 . RNA helicases are found in all three domains of life, and many viruses also encode one or more of these proteins 2,3 . Together with the structurally related DNA helicases that function in replication, recombination and repair, the RNA helicases are classified into superfamilies and families, based on sequence and structural features 3,4 . DEAD box proteins form the largest helicase family, with 37 members in humans and 26 in Saccharomyces cerevisiae 3 , and are characterized by the presence of an Asp-Glu-Ala-Asp (DEAD) motif.DEAD box helicases have central and, in many cases, essential physiological roles in cellular RNA metabolism 5 (FIG. 1). The proteins generally function as part of larger multicomponent assemblies, such as the spliceosom e or the eukaryotic translation initiation machinery 6 . Mutations and deregulation of several DEAD box proteins have been linked to disease states, including cancer 7 . Although all DEAD box proteins contain a structurally highly conserved core with conserved ATP-binding and RNA-binding sites, different proteins have been associated with diverse and seemingly unrelated functions, including the disassembly of RNPs, chaperoning during RNA folding and even stabil ization of protein complexes on RNA 5,6 . How these highly conserved proteins fulfil such an array of different functions has been a long-standing question.Research has now started to illuminate the molecular basis for this functional diversity. In this Review, we summarize how structural data, together with biochemical and biophysical studies, have revealed unexpected modes by which these proteins function. We also discuss how novel molecular and cell biological approaches have better defined the cellular roles of DEAD box helicases. We outline our current view on common structural and mechan istic themes that have emerged, and on physical models of how these 'unusual' RNA helicases work.Structures of DEAD box RNA helicases A number of structural studies have universally shown that members of the DEAD box family contain a highly conserved helicase core that harbours the binding sites for ATP and RNA 3,4,8 . The core is surrounded by variable auxiliary domains, which are thought to be critical for the diverse functions of these enzymes.Structure of the helicase core. DEAD box proteins belong to helicase superfamily 2 (SF2) 2 . Similarly to all SF2 helicases, DEAD box proteins are built around a highly conserved helicase core of two virtually identical domains that resemble the bacterial recombination protein recombinase A (RecA) 3,4,8 (FIG. 2a,b). Within this helicase core, at least 12 characteristic sequence motifs are located at conserved positions (FIG. 2a,b). Some of these motifs are conserved across the entire SF2 family, whereas others are found only in the DEAD box family 3 ....

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Section: Mitochondrial Rna Editingmentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

983

1,069

View full text Add to dashboard Cite

show abstract

“…Consistent with this idea, a multitude of DEAD-box proteins are required in processes that use guide RNAs to perform RNA modification, RNA processing, or RNA editing. Moreover, genetic evidences suggest that DEAD-box proteins are indeed required for dissociation of guide RNA containing complexes in vivo (Chen et al, 2001;Kistler and Guthrie, 2001). Nevertheless, a bona fide dsRNA dissociation activity in vivo is extremely difficult to demonstrate.…”

Section: Introductionmentioning

confidence: 99%

DEAD-Box RNA Helicases in Gram-Positive RNA Decay

Redder

Linder

2012

Methods in Enzymology

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“…The replacement of the U1 snRNA with the U6 snRNA at the 59 splice is believed to activate the spliceosome, bringing the catalytic site in close proximity of the 59 splice site+ This step is facilitated by a number of spliceosomal components+ The RNA helicase Prp28 appears to be involved in the removal of the U1 snRNA from the 59 splice site+ This is mainly based on the observations in S. cerevisiae showing that Prp28 is required for the first step of splicing (Strauss & Guthrie, 1994) and that this requirement is bypassed by mutations in the U1 snRNP-specific protein U1C (Chen et al+, 2001)+ Moreover, Prp28 mutants produce a synthetic lethal phenotype with mutations in the U1 snRNA that hyperstabilize the U1 snRNA/59 splice site interaction in yeast (Staley & Guthrie, 1999)+ Also the human homolog of Prp28, U5-100kD, is in close contact with the 59 splice site (Ismaili et al+, 2001)+ Thus, Prp28 probably functions by counteracting the stabilizing effect of U1C on the U1 snRNA/59 splice site interaction+…”

Section: Introductionmentioning

confidence: 99%

Defining a 5??? splice site by functional selection in the presence and absence of U1 snRNA 5??? end

Lund

Kjems

2002

RNA

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Pre-mRNA splicing in metazoans is mainly specified by sequences at the termini of introns. We have selected functional 59 splice sites from randomized intron sequences through repetitive rounds of in vitro splicing in HeLa cell nuclear extract. The consensus sequence obtained after one round of selection in normal extract closely resembled the consensus of natural occurring 59 splice sites, suggesting that the selection pressures in vitro and in vivo are similar. After three rounds of selection under competitive splicing conditions, the base pairing potential to the U1 snRNA increased, yielding a G 100% U 100% R 94% A 67% G 89% U 76% R 83% intronic consensus sequence. Surprisingly, a nearly identical consensus sequence was obtained when the selection was performed in nuclear extract containing U1 snRNA with a deleted 59 end, suggesting that other factors than the U1 snRNA are involved in 59 splice site recognition. The importance of a consecutive complementarity between the 59 splice site and the U1 snRNA was analyzed systematically in the natural range for in vitro splicing efficiency and complex formation. Extended complementarity was inhibitory to splicing at a late step in spliceosome assembly when pre-mRNA substrates were incubated in normal extract, but favorable for splicing under competitive splicing conditions or in the presence of truncated U1 snRNA where transition from complex A to complex B occurred more rapidly. This suggests that stable U1 snRNA binding is advantageous for assembly of commitment complexes, but inhibitory for the entry of the U4/U6.U5 trisnRNP, probably due to a delayed release of the U1 snRNP.

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Specific Alterations of U1-C Protein or U1 Small Nuclear RNA Can Eliminate the Requirement of Prp28p, an Essential DEAD Box Splicing Factor

Cited by 191 publications

References 43 publications

From unwinding to clamping — the DEAD box RNA helicase family

From unwinding to clamping — the DEAD box RNA helicase family

DEAD-Box RNA Helicases in Gram-Positive RNA Decay

Defining a 5??? splice site by functional selection in the presence and absence of U1 snRNA 5??? end

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