A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya

Kaya, Yusuf; Ofengand, James

doi:10.1261/rna.5230603

Cited by 99 publications

(108 citation statements)

References 49 publications

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“…Pseudouridine synthases are best characterized in E. coli, in which there are 11 family members. These enzymes mediate uridine-to-C isomerization in tRNAs (designated Tru genes) and rRNAs (designated Rlu genes, for ribosomal 50S rRNAs, and Rsu genes, for ribosomal 30S rRNAs) (Koonin, 1996;Ofengand, 2002;Kaya and Ofengand, 2003). E. coli pseudouridine synthases diverge widely in amino acid sequence, yet they fold into similar structures (Mueller, 2002).…”

Section: Svr1 Encodes a Pseudouridine Synthasementioning

confidence: 99%

Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis

et al. 2008

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The Arabidopsis thaliana yellow variegated2 (var2) mutant is variegated due to lack of a chloroplast FtsH-like metalloprotease (FtsH2/VAR2). We have generated suppressors of var2 variegation to gain insight into factors and pathways that interact with VAR2 during chloroplast biogenesis. Here, we describe two such suppressors. Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (C) synthase, which isomerizes uridine to C in noncoding RNAs. svr1 single mutants were epistatic to var2, and they displayed a phenotypic syndrome that included defects in chloroplast rRNA processing, reduced chloroplast translation, reduced chloroplast protein accumulation, and elevated chloroplast mRNA levels. In the second line (TAG-IE), suppression of variegation was caused by a lesion in SVR2, the gene for the ClpR1 subunit of the chloroplast ClpP/R protease. Like svr1, svr2 was epistatic to var2, and clpR1 mutants had a phenotype that resembled svr1. We propose that an impairment of chloroplast translation in TAG-FN and TAG-IE decreased the demand for VAR2 activity during chloroplast biogenesis and that this resulted in the suppression of var2 variegation. Consistent with this hypothesis, var2 variegation was repressed by chemical inhibitors of chloroplast translation. In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation.

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Section: Svr1 Encodes a Pseudouridine Synthasementioning

confidence: 99%

Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis

et al. 2008

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“…Based on structural and sequence homologies, pseudouridylases are classified into 5 families, RluA, RsuA, TruA, TruB, and TruD [10].…”

Section: The Structuresmentioning

confidence: 99%

“…Based on structural and sequence homologies, pseudouridylases are classified into 5 families, RluA, RsuA, TruA, TruB, and TruD [10]. Crystal structures of bacterial and/or archaeal representatives for each family have been solved.…”

Section: The Structuresmentioning

confidence: 99%

How a single protein complex accommodates many different H/ACA RNAs

Meier

2006

Trends in Biochemical Sciences

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Over 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins. The function of these H/ACA RNPs is essential for ribosome biogenesis, pre-mRNA splicing, telomere maintenance, and, likely, for additional cellular processes. Recent crystal structures of archaeal H/ACA protein complexes illustrate how the same four proteins accommodate more than 100 distinct though related H/ACA RNAs and reveal a spatial mutation cluster underlying the bone marrow failure syndrome dyskeratosis congenita (DC).Keywords H/ACA RNPs; H/ACA RNAs; crystal structure; core proteins; dyskeratosis congenita; RNAprotein interaction The vast majority of mammalian H/ACA RNPs engage in isomerization of uridines to pseudouridines (pseudouridylation) in ribosomal and spliceosomal small nuclear RNAs. Although the function of most pseudouridines is unknown, some are essential for optimal translation and for pre-mRNA splicing [1]. Perhaps the most intriguing species of H/ACA RNPs are defined by the snoRNA U17/E1 (snR30 in yeast), telomerase RNA (which ends in an H/ACA RNA structure), and a growing number of orphan H/ACA RNAs (without complementarity to any stable RNAs) [2]. U17 is the only essential H/ACA RNA and is required for pre-ribosomal RNA processing; telomerase RNA is required for the replication of chromosome ends; and the orphan H/ACA RNAs are by definition of unknown function but potentially involved in similar important processes as U17 and telomerase RNA (Fig. 1) [3]. Recently, three groups solved the crystal structures of archaeal H/ACA RNP core complexes consisting of two or three core proteins (Fig. 1) [4][5][6]. For the first time, these structures provide molecular details of protein-protein interactions in the H/ACA core complex and of the pseudouridylase itself. meier@aecom.yu Fig. 1), the other class being C/D RNAs. On average 130-140 nucleotides in length, H/ACA RNAs conform to a consensus 5'-hairpin-hinge-hairpin-tail-3' secondary structure with the characteristic ACA trinucleotide exactly three residues from the 3' end ( Fig. 1). H/ACA RNAs identify the ~130 known mammalian pseudouridylation sites by base pairing to a few nucleotides flanking the target uridines. Complementarity to target RNAs lies in the upper half of a bulge (pseudouridylation pocket) of one or both of the hairpins placing the unpaired target uridine at the bottom of a helix [7,8]. Pseudouridylation is catalyzed by one of the four H/ACA core proteins, the pseudouridylase NAP57 (also dyskerin or, in yeast and archaea, Cbf5) [9]. The small basic proteins GAR1, NOP10, and NHP2 (L7Ae in archaea) round out H/ACA RNPs. All four core proteins, except GAR1, are essential for the structural integrity of H/ACA RNPs [3]. The structuresThe structure of the archaeal pseudouridylase Cbf5 was solved complexed with Nop10 [5,6] or with Nop10 and Gar1 [4]. Based on structural and sequence homologies, pseudouridylases are classified into 5 families, RluA, RsuA, TruA, TruB, and TruD [10].Crystal structur...

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“…The contribution to cell physiology by individual pseudouridine synthases and the C residues for which each is responsible has been investigated in our laboratory by deletion of their respective genes. Mutant E. coli strains lacking the individual synthases, RsuA , RluA (Raychaudhuri et al 1999), RluC , TruB (Gutgsell et al 2000), RluB, RluE, RluF, and TruC (Del Campo et al 2001), and TruD (Kaya and Ofengand 2003) have been characterized. Of these, only the loss of the rluA (C746 23S rRNA and C32 tRNA phe ) and the truB (C55 all tRNAs) synthase genes were shown to result in a demonstrable growth phenotype as evidenced by reduced survival in competition with wild-type E. coli.…”

Section: Introductionmentioning

confidence: 99%

The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli

Gutgsell

Deutscher²,

Ofengand

2005

RNA

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RluD is the pseudouridine synthase responsible for the formation of C1911, C1915, and C1917 in Escherichia coli 23S rRNA. Previous work from our laboratory demonstrated that disruption of the rluD gene and/or loss of the pseudouridine residues for which it is responsible resulted in a severe growth phenotype. In the current work we have examined further the effect of the loss of the RluD protein and its product pseudouridine residues in a deletion strain lacking the rluD gene. This strain exhibits defects in ribosome assembly, biogenesis, and function. Specifically, there is a deficit of 70S ribosomes, an increase in 50S and 30S subunits, and the appearance of new 62S and 39S particles. Analysis of the 39S particles indicates that they are immature precursors of the 50S subunits, whereas the 62S particles are derived from the breakdown of unstable 70S ribosomes. In addition, purified mutant 70S ribosomes were found to be somewhat less efficient than wild type in protein synthesis. The defect in ribosome assembly and resulting growth phenotype of the mutant could be restored by expression of wild-type RluD and synthesis of C1911, C1915, and C1917 residues, but not by catalytically inactive mutant RluD proteins, incapable of pseudouridine formation. The data suggest that the loss of the pseudouridine residues can account for all aspects of the mutant phenotype; however, a possible second function of the RluD synthase is also discussed.

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A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya

Cited by 99 publications

References 49 publications

Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis

Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis

How a single protein complex accommodates many different H/ACA RNAs

The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli

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