Long-distance placement of substrate RNA by H/ACA proteins

Liang, Bo; Kahen, Elliot; Calvin, Kate; Zhou, Jing; Blanco, Mario R.; Liang, Hong

doi:10.1261/rna.1109808

Cited by 22 publications

(31 citation statements)

References 41 publications

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“…In the RNA-guided pseudouridylation reaction, the guide RNA uses its internal loop to capture substrate RNA through base-pairing. The four protein subunits all participate in the process of substrate RNA placement (Liang et al 2007(Liang et al , 2008(Liang et al , 2009). The protein subunits interact with the guide RNA in specific manners to tightly anchor it on the surface of Cbf5 such that the substrate RNA is correctly placed in the active site (Li and Ye 2006;Liang et al 2007Liang et al , 2009Duan et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide

Zhou¹,

Liang²,

Li³

2010

RNA

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Cbf5 is the catalytic subunit of the H/ACA small nucleolar/Cajal body ribonucleoprotein particles (RNPs) responsible for site specific isomerization of uridine in ribosomal and small nuclear RNA. Recent evidence from studies on archaeal Cbf5 suggests its second functional role in modifying tRNA U55 independent of guide RNA. In order to act both as a stand-alone and a RNP pseudouridine synthase, Cbf5 must differentiate features in H/ACA RNA from those in tRNA or rRNA. Most H/ACA RNAs contain a hallmark ACA trinucleotide downstream of the H/ACA motif. Here we challenged an archaeal Cbf5 (in the form of a ternary complex with its accessory proteins Nop10 and Gar1) with T-stem-loop RNAs with or without ACA trinucleotide in the stem. Although these substrates were previously shown to be substrates for the bacterial stand-alone pseudouridine synthase TruB, the Cbf5-Nop10-Gar1 complex was only able to modify those without ACA trinucleotide. A crystal structure of Cbf5-Nop10-Gar1 trimer bound with an ACA-containing T-stem-loop revealed that the ACA trinucleotide detracted Cbf5 from the stand-alone binding mode, thereby suggesting that the H/ACA RNP-associated function of Cbf5 likely supersedes its stand-alone function.

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Section: Discussionmentioning

confidence: 99%

Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide

Zhou¹,

Liang²,

Li³

2010

RNA

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“…Liang et al (25,42) employed fluorescence spectroscopy to monitor productive docking of the substrate RNA into the active RNP and found that L7Ae is a key player. Comparison of the crystal structures of the guide RNA-substrate RNA complex bound to Cbf5-Nop10 with (20,21) and without (25) L7Ae reveals markedly different RNA conformations.…”

Section: Role Of Proteins In Rna Remodelingmentioning

confidence: 99%

“…These data tentatively implicate Gar1 in product release. Fluorescence spectroscopic analysis of the RNP showed that whereas L7Ae promotes formation of the active structure of the RNP, Gar1 does the opposite (42). Gar1 may serve to stabilize the undocked inactive conformation of the RNP by biasing the thumb loop to its open conformation.…”

Section: Active Site and Enzymatic Turnovermentioning

confidence: 99%

The Box H/ACA Ribonucleoprotein Complex: Interplay of RNA and Protein Structures in Post-transcriptional RNA Modification

Hamma

Ferré-D′Amaré

2010

Journal of Biological Chemistry

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The box H/ACA ribonucleoproteins (RNPs) are protein-RNA complexes responsible for pseudouridylation, the most abundant post-transcriptional modification of cellular RNAs. Integrity of its box H/ACA domain is also essential for assembly and stability of the human telomerase RNP. The recent publication of the complete box H/ACA RNP structures combined with the previously reported structures of the protein and RNA components makes it possible to deduce the structural accommodation that accompanies assembly of the full particle. This analysis reveals how the protein components distort the RNA component of the RNP, enabling productive docking of the substrate RNA into the enzymatic active site.Cellular RNAs undergo numerous site-specific post-transcriptional modifications. Over 100 chemically distinct modified nucleotides have been identified (the RNA Modification Database (1) and the Modomics Database (2)). The most abundant is ⌿, 2 the C-5 glycoside isomer of uridine. The isomerization of U residues into ⌿ is performed by universally distributed enzymes called ⌿ synthases, which can be classified into two groups depending on their substrate recognition mechanism. First, a number of ⌿ synthases composed of a single polypeptide recognize their substrate RNAs with high specificity and also catalyze the isomerization reaction. Second, the ⌿ synthase Cbf5/dyskerin associates with three additional polypeptides and a guide RNA (which is responsible for site specificity) to form an RNP. These guide RNAs are characterized by a conserved secondary structure and two closely related sequence elements called "box H" and "box ACA," hence the name of the RNP (reviewed in Refs. 3-5).

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“…The thumb loop of Cbf5, also called the β7_10 loop, is located between its β7 and β10 strands (Li and Ye 2006;Liang et al 2008Liang et al , 2009Duan et al 2009;Hamma and Ferré-D'Amaré 2010;Li et al 2011). It interacts with the Gar1 protein and the substrate RNA but not with the guide RNA.…”

Section: Introductionmentioning

confidence: 99%

Structure–function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation

Majumder

Bosmeny

Gupta

2016

RNA

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In Eukarya and Archaea, in addition to protein-only pseudouridine (Ψ) synthases, complexes containing one guide RNA and four proteins can also produce Ψ. Cbf5 protein is the Ψ synthase in the complex. Previously, we showed that Ψ's at positions 1940, 1942, and 2605 of Haloferax volcanii 23S rRNA are absent in a cbf5-deleted strain, and a plasmid-borne copy of cbf5 can rescue the synthesis of these Ψ's. Based on published reports of the structure of archaeal Cbf5 complexed with other proteins and RNAs, we identified several potential residues and structures in H. volcanii Cbf5, which were expected to play important roles in pseudouridylation. We mutated these structures and determined their effects on Ψ production at the three rRNA positions under in vivo conditions. Mutations of several residues in the catalytic domain and certain residues in the thumb loop either abolished Ψ's or produced partial modification; the latter indicates a slower rate of Ψ formation. The universal catalytic aspartate of Ψ synthases could be replaced by glutamate in Cbf5. A conserved histidine, which is common to Cbf5 and TruB is not needed, but another conserved histidine of Cbf5 is required for the in vivo RNA-guided Ψ formation. We also identified a previously unreported novelty in the pseudouridylation activity of Cbf5 where a single stem-loop of a guide H/ACA RNA is used to produce two closely placed Ψ's and mutations of certain residues of Cbf5 abolished one of these two Ψ's. In summary, this first in vivo study identifies several structures of an archaeal Cbf5 protein that are important for its RNAguided pseudouridylation activity.

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Long-distance placement of substrate RNA by H/ACA proteins

Cited by 22 publications

References 41 publications

Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide

Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide

The Box H/ACA Ribonucleoprotein Complex: Interplay of RNA and Protein Structures in Post-transcriptional RNA Modification

Structure–function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation

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