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Frontiers in Biology

Front. Biol.    2018, Vol. 13 Issue (1) : 1-10     https://doi.org/10.1007/s11515-018-1480-8
REVIEW
RNA-dependent pseudouridylation catalyzed by box H/ACA RNPs
Meemanage D. De Zoysa, Yi-Tao Yu()
University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY14642, USA
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Abstract

BACKGROUND: Pseudouridine (Y) is the most abundant post-transcriptionally modified nucleotide found in RNA. Y is clustered in functionally important and evolutionary conserved regions of RNAs in all three domains of life. Pseudouridylation is catalyzed by two distinct mechanisms: an RNA-independent and an RNA-dependent mechanism. The former involves a group of stand-alone protein enzymes, and the latter involves a family of complex enzymes called box H/ACA RNPs, each of which consists of one RNA (box H/ACA RNA) and a set of four core proteins. Over the years, the mechanism of RNA-dependent pseudouridylation has been extensively studied. The crystal structures of partial and complete box H/ACA RNP have been solved. However, the detailed picture of RNA-dependent pseudouridylation is still not entirely clear.

OBJECTIVE: In this work, we review what is known about box H/ACA RNP and the mechanism by which box H/ACA RNP catalyzes RNA-dependent pseudouridylation. We also discuss some examples of the dual nature and redundancy of box H/ACA RNPs that deviate from the usual mechanism.

METHODS: A methodical literature search was performed using the Pubmed central search engine and International Digital Publishing Forum (EPUB) using the following keywords: “pseudouridylation,” “pseudouridine,” and “box H/ACA RNP.” The necessary information was extracted and cited.

RESULTS: A detailed introduction is made including the discovery, mechanism and crystal structure of box H/ACA RNP. Three sequence/structural requirements for box H/ACA RNA-guided pseudouridylation are discussed and the exceptions to those rules are explored.

CONCLUSION: Over the years, box H/ACA RNP-catalyzed pseudouridylation has been extensively studied, generating fruitful results. However, a detailed picture regarding the mechanism of this reaction is still to be deciphered. More work is needed to fully understand box H/ACA RNP-catalyzed pseudouridylation.

Corresponding Author(s): Yi-Tao Yu   
Just Accepted Date: 19 January 2018   Issue Date: 26 March 2018
 Cite this article:   
Meemanage D. De Zoysa,Yi-Tao Yu. RNA-dependent pseudouridylation catalyzed by box H/ACA RNPs[J]. Front. Biol., 2018, 13(1): 1-10.
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http://journal.hep.com.cn/fib/EN/10.1007/s11515-018-1480-8
http://journal.hep.com.cn/fib/EN/Y2018/V13/I1/1
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Meemanage D. De Zoysa
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Fig.1  Pseudouridylation (U-to-Y Isomerization). The nucleotide pseudouridylation reaction is schematized. The N1-C1' bond in uridine is broken. The uracil base is lifted up and turned 180° around the C6-N3 axis. Upon reformation of the C5-C1' bond, Y is generated. “a” and “d” represent hydrogen bond acceptor and donor, respectively.
Fig.2  Box H/ACA RNP, a highly complex pseudouridylase that catalyzes RNA-dependent RNA pseudouridylation. The components of the RNP, including a box H/ACA RNA and four core proteins (Cbf5, Nhp2, Nop10 and Gar1), are shown. The two hairpins, the hinge region and the 3′ ACA tail of the box H/ACA RNA are indicated. The upper and lower stems, as well as the internal loop (or pseudouridylation pocket) of each hairpin are also indicated. Also depicted are the substrate RNA, which forms base-pairing interactions with the pseudouridylation pocket sequences, and the target uridines, which are to be pseudouridylated (Ys, the arrows).
Fig.3  Box H/ACA RNA-guided RNA pseudouridylation under normal and stress conditions. Shown is the S. cerevisiae snR81 box H/ACA RNA, which guides the pseudouridylation of U2 snRNA at position 42 (the 5′ pocket) and 25 S rRNA at position 1051 (the 3′ pocket) under normal and starvation conditions. Under starvation conditions, the 3′ pocket of snR81 loosens its specificity to also guide U2 pseudouridylation at a novel site, position 93. The substrate RNAs (U2 snRNA and 25S rRNA), which form base-pairing interactions with the sequences of the pseudouridylation pockets, and the target nucleotides to be pseudouridylated (Ys, the arrows) are also shown. The H and ACA boxes of snR81 are indicated (gray boxes) as well.
Fig.4  Intricate box H/ACA RNA-substrate network. Several mammalian box H/ACA RNAs, including ACA19, ACA42 and ACA67, are schematized. According to computational predictions, the 5′ hairpin of ACA19 folds into three alternative structures, forming three distinct pseudouridylation pockets that target three different sites, U866 and U863 of 18S rRNA and U3709 of 28S rRNA. However, experimental results indicate that the 5′ pocket of ACA19 only targets U3709 of 28S rRNA (Xiao et al., 2009). U866 and U863 of 18S rRNA are the targets of ACA28 (its 3′ pocket) and ACA24 (its 5′ pocket), respectively (indicated) (Xiao et al., 2009). Based on computational predictions, ACA42 and ACA67 possess almost identical pseudouridylation pockets, targeting the same sites: the 5′ pocket of ACA42 and the 5′ pocket of ACA67 both target U572 of 18S rRNA, and the ACA42 3′ pocket and the ACA67 3′ pocket both target U109 of 18S rRNA. But, in reality, the 5′ pocket of ACA42 fails to guide U572-to-Y572 conversion (Xiao et al., 2009). Interestingly, small nucleotide changes can turn a non-functional pseudouridylation pocket into a functional pocket.
Fig.5  Redundancy between stand-alone pseudouridine synthases and box H/ACA RNP pseudouridylases. Vertebrate U2 RNA is schematized and its branch site recognition region sequence is shown. Pus7 (stand-alone protein enzyme) and the 5′ pocket of pugU2-34/44 (a box H/ACA RNP also known as SCARNA8 or U92 scaRNP) both target U34 (equivalent to U35 in Drosophila) of U2. Pus1 (stand-alone protein enzyme) and pugU2-34/44 (or pugU2-43/44 in pombe) both target U43 (equivalent to U44 in Drosophila) of U2 (Deryusheva and Gall, 2017).
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