The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing

Jackson, Ryan N.; Klauer, A. Alejandra; Hintze, Bradley J.; Robinson, Howard; Hoof, Ambro van; Johnson, Sean

doi:10.1038/emboj.2010.107

Cited by 108 publications

(215 citation statements)

References 66 publications

Supporting

Mentioning

200

Contrasting

Order By: Relevance

“…3). These findings suggest common functional features in Ski2-like and DEAH/RHA helicases, consistent with structural conservation in the C termini of both helicase families, and the presence of a conserved β-hairpin between the helicase motifs Va and VI in Ski2-like, DEAH/RHA, and viral NS3/NPH-II helicases (14,(27)(28)(29)(30)(31)(32)(33)(34). However, given that no activity was seen in single-cycle experiments with both Mtr4p and TRAMP, it would be premature to extrapolate from the available data that Mtr4p/TRAMP unwind duplexes by processive translocation.…”

Section: Discussionmentioning

confidence: 48%

RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex

Jia

Wang

Anderson

et al. 2012

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

View full text Add to dashboard Cite

Many RNA-processing events in the cell nucleus involve the Trf4/ Air2/Mtr4 polyadenylation (TRAMP) complex, which contains the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for processing by the nuclear exosome. In addition, TRAMP functions as an exosome cofactor during RNA degradation, and it has been speculated that this role involves disruption of RNA secondary structure. However, it is unknown whether TRAMP displays RNA unwinding activity. It is also not clear how unwinding would be coordinated with polyadenylation and the function of the RNA helicase Mtr4p in modulating poly(A) addition. Here, we show that TRAMP robustly unwinds RNA duplexes. The unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p, but the stimulation of Mtr4p does not depend on ongoing polyadenylation. Nonetheless, polyadenylation enables TRAMP to unwind RNA substrates that it otherwise cannot separate. Moreover, TRAMP displays optimal unwinding activity on substrates with a minimal Mtr4p binding site comprised of adenylates. Our results suggest a model for coordination between unwinding and polyadenylation activities by TRAMP that reveals remarkable synergy between helicase and poly(A) polymerase.he Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex is involved in nuclear RNA surveillance, 3′-end processing of rRNA, small nucleolar RNAs (snoRNAs), and snRNAs, and in gene silencing and chromatin maintenance (1-3). The TRAMP complex consists of three subunits that are highly conserved in eukaryotes: a noncanonical poly(A) polymerase (Trf4p or Trf5p in Saccharomyces cerevisiae), a Zn-knuckle protein (Air2p or Air1p), and the RNA helicase Mtr4p (4-7). TRAMP assists RNA degradation by the nuclear exosome, most notably by appending short (∼4-5 nt) oligo(A) tails at the 3′ ends of RNAs slated for exosome-mediated degradation (4,5,(8)(9)(10). In addition, it has been speculated that TRAMP enables the nuclear exosome to efficiently degrade structured RNA through unwinding activity associated with Mtr4p (1, 2, 11-13).However, RNA helicase activity has not been demonstrated for TRAMP. Though Mtr4p alone has been shown to unwind RNA duplexes in vitro (12, 13), it is not known whether binding of Trf4p/Air2p abolishes, decreases, increases, or otherwise alters this helicase activity. This question is important for TRAMP function, because Mtr4p and Trf4p operate with opposite polarities. Mtr4p only unwinds duplexes with a 3′ unpaired region, i.e., with a 3′ to 5′ polarity (12, 13). Trf4p polyadenylates the 3′ end of RNA and thus possesses 5′ to 3′ polarity (4, 5). How unwinding and polyadenylation with opposite polarities are coordinated in one complex is not readily apparent.Moreover, Mtr4p controls the lengths of poly(A) tails appended by TRAMP (9). This role of Mtr4p requires ATP, but does not involve unwinding (9). Instead, Mtr4p binds to the 3′ end of the RNA, detects the number of 3′-terminal adenosines, and, in response, modulates ATP affinity and adenylatio...

show abstract

Section: Discussionmentioning

confidence: 48%

RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex

Jia

Wang

Anderson

et al. 2012

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

View full text Add to dashboard Cite

show abstract

“…A similar Gln‐based specificity determinant for adenine nucleotides was originally identified in the so‐called Q motif of DEAD‐box proteins (Cordin et al , 2004). Although at the sequence level the corresponding Q motif of Upf1‐like helicases is also present upstream of motif I, at the three‐dimensional level it forms part of a different structural element as compared to the Q motif of DEAD‐box proteins and is instead similar to the Q motif found in the Ski2‐like family of DExH‐box proteins (Sengoku et al , 2006; Jackson et al , 2010; Weir et al , 2010). …”

Section: Resultsmentioning

confidence: 99%

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

et al. 2017

View full text Add to dashboard Cite

The superfamily 1B (SF1B) helicase Sen1 is an essential protein that plays a key role in the termination of non‐coding transcription in yeast. Here, we identified the ~90 kDa helicase core of Saccharomyces cerevisiae Sen1 as sufficient for transcription termination in vitro and determined the corresponding structure at 1.8 Å resolution. In addition to the catalytic and auxiliary subdomains characteristic of the SF1B family, Sen1 has a distinct and evolutionarily conserved structural feature that “braces” the helicase core. Comparative structural analyses indicate that the “brace” is essential in shaping a favorable conformation for RNA binding and unwinding. We also show that subdomain 1C (the “prong”) is an essential element for 5′‐3′ unwinding and for Sen1‐mediated transcription termination in vitro. Finally, yeast Sen1 mutant proteins mimicking the disease forms of the human orthologue, senataxin, show lower capacity of RNA unwinding and impairment of transcription termination in vitro. The combined biochemical and structural data thus provide a molecular model for the specificity of Sen1 in transcription termination and more generally for the unwinding mechanism of 5′‐3′ helicases.

show abstract

“…In these enzymes, the N-terminal extensions seem to stabilize an inactive relative orientation of the 2 RecA-like domains, with the surfaces that have to come together for ATP and RNA binding remote from each other. In contrast, the N-terminal extensions of Prp43, 58,59,71 yeast Mtr4 68,69 and Neurospora crassa frequency-interacting RNA helicase (FRH) 78 together with accessory domains stabilize a relative orientation of the RecA-domains that resembles the productive conformation (Fig. 3D-F).…”

Section: Layer III -The Ntr As An Auto-inhibition Devicementioning

confidence: 99%

“…However, additional domains are restricted to individual proteins or sub-groups of helicases. E.g., while the Ski2-like DNA helicase, Hel308, contains a HLH domain (which improves coupling of ATPase and unwinding activities 67 ) following the ratchet domain as also seen in Brr2, the Ski2-like RNA helicase, Mtr4, contains an arch-like domain inserted into its core (which aids in the recognition of specific substrates 68,69 and modulates helicase activity 70 ). The DEAH/RHA helicases Prp2, Prp16, Prp22 and Prp43, in contrast, contain a C-terminal OBfold, 58,59,71,72 which in Prp43 stimulates RNA binding and ATPase activity.…”

Section: Layer III -The Ntr As An Auto-inhibition Devicementioning

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

The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing

Cited by 108 publications

References 66 publications

RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex

RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

Functions and regulation of the Brr2 RNA helicase during splicing

Contact Info

Product

Resources

About