Solution structure of  32-modified anticodon stem-loop of Escherichia coli tRNAPhe

Cabello-Villegas, Javier; Nikonowicz, Edward P.

doi:10.1093/nar/gki1004

Cited by 30 publications

(30 citation statements)

References 50 publications

(69 reference statements)

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“…Pseudouridines are believed to confer extra stability and rigidity to the local RNA structure surrounding the modified base (Davis et al 1998;Cabello-Villegas and Nikonowicz 2005). Consistent with these observations, pseudouridines are found in highly structured RNA species whose tertiary structure is important for their function (including tRNA, rRNA, snRNA, and tmRNA); they are usually absent in mRNA (Charette and Gray 2000), though they have been observed in the leader sequences that are trans-spliced onto all mRNAs in trypanosomes (Liang et al 2002).…”

Section: Introductionmentioning

confidence: 85%

RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA

Vaidyanathan

Deutscher²,

Malhotra³

2007

RNA

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Pseudouridine modifications in helix 69 (H69) of 23S ribosomal RNA are highly conserved among all organisms. H69 associates with helix 44 of 16S rRNA to form bridge B2a, which plays a vital role in bridging the two ribosomal subunits and stabilizing the ribosome. The three pseudouridines in H69 were shown earlier to play an important role in 50S subunit assembly and in its association with the 30S subunit. In Escherichia coli, these three modifications are made by the pseudouridine synthase, RluD. Previous work showed that RluD is required for normal ribosomal assembly and function, and that it is the only pseudouridine synthase required for normal growth in E. coli. Here, we show that RluD is far more efficient in modifying H69 in structured 50S subunits, compared to free or synthetic 23S rRNA. Based on this observation, we suggest that pseudouridine modifications in H69 are made late in the assembly of 23S rRNA into mature 50S subunits. This is the first reported observation of a pseudouridine synthase being able to modify a highly structured ribonucleoprotein particle, and it may be an important late step in the maturation of 50S ribosomal subunits.

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Section: Introductionmentioning

confidence: 85%

RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA

Vaidyanathan

Deutscher²,

Malhotra³

2007

RNA

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“…5,9,[45][46][47] The one-dimensional spectrum recorded in water exhibited three sharp resonances in the imino region, which were assigned to the imino resonances of the three guanines of the stem, G 41 , G 31 and G 30 , all involved in canonical G·C base pairing. Two other resonances, broader than the previous signals, were assigned to G 43 H1 and U 28 H3.…”

Section: Nmr Resonances Assignmentsmentioning

confidence: 99%

Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2

Cantara

Bilbille

Kim

et al. 2012

Journal of Molecular Biology

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“…In this way, Ψ's can stabilize tRNA folding and increase the fidelity of codon-anticodon interactions, stabilize certain stem-loop conformations of snRNAs, and enable ribosome assembly (Yarian et al 1999;Greenbaum 2001, 2002b;Nobles et al 2002;Cabello-Villegas and Nikonowicz 2005;Denmon et al 2011;Jack et al 2011;Penzo et al 2015). The majority of indications that pseudouridylation plays an important biological role stems indirectly from the observation that Ψ's are modulated in response to different cellular conditions.…”

Section: Introductionmentioning

confidence: 99%

mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii

Nakamoto

Lovejoy

Cygan

et al. 2017

RNA

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RNA contains over 100 modified nucleotides that are created post-transcriptionally, among which pseudouridine (Ψ) is one of the most abundant. Although it was one of the first modifications discovered, the biological role of this modification is still not fully understood. Recently, we reported that a pseudouridine synthase (TgPUS1) is necessary for differentiation of the singlecelled eukaryotic parasite Toxoplasma gondii from active to chronic infection. To better understand the biological role of pseudouridylation, we report here gel-based and deep-sequencing methods to identify TgPUS1-dependent Ψ's in Toxoplasma RNA, and the use of TgPUS1 mutants to examine the effect of this modification on mRNAs. In addition to identifying conserved sites of pseudouridylation in Toxoplasma rRNA, tRNA, and snRNA, we also report extensive pseudouridylation of Toxoplasma mRNAs, with the Ψ's being relatively depleted in the 3 ′ ′ ′ ′ ′ -UTR but enriched at position 1 of codons. We show that many Ψ's in tRNA and mRNA are dependent on the action of TgPUS1 and that TgPUS1-dependent mRNA Ψ's are enriched in developmentally regulated transcripts. RNA-seq data obtained from wild-type and TgPUS1-mutant parasites shows that genes containing a TgPUS1-dependent Ψ are relatively more abundant in mutant parasites, while pulse/chase labeling of RNA with 4-thiouracil shows that mRNAs containing TgPUS1-dependent Ψ have a modest but statistically significant increase in half-life in the mutant parasites. These data are some of the first evidence suggesting that mRNA Ψ's play an important biological role.

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Solution structure of 32-modified anticodon stem-loop of Escherichia coli tRNAPhe

Cited by 30 publications

References 50 publications

RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA

RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA

Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2

mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii

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