Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF

Abstract

Pseudouridine is found in almost all cellular ribonucleic acids (RNAs). Of the multiple characteristics attributed to pseudouridine, making messenger RNAs (mRNAs) highly translatable and non-immunogenic is one such feature that directly implicates this modification in protein synthesis. We report the existence of pseudouridine in the anticodon of Escherichia coli tyrosine transfer RNAs (tRNAs) at position 35. Pseudouridine was verified by multiple detection methods, which include pseudouridine-specific chemical derivatization and gas phase dissociation of RNA during liquid chromatography tandem mass spectrometry (LC-MS/MS). Analysis of total tRNA isolated from E. coli pseudouridine synthase knock-out mutants identified RluF as the enzyme responsible for this modification. Furthermore, the absence of this modification compromises the translational ability of a luciferase reporter gene coding sequence when it is preceded by multiple tyrosine codons. This effect has implications for the translation of mRNAs that are rich in tyrosine codons in bacterial expression systems.Of 150-plus chemical modifications (1, 2) found in cellular RNA, 5-ribosyluridine or pseudouridine (⌿) 3 (3) is the most abundant but still poorly understood (4) modification. Pseudouridine, which has been found in the functionally important regions of RNAs (5), is known to modulate codon-anticodon interactions between mRNA and tRNA (6) and assist assembly of the ribosome (7) and spliceosome (8). The presence of pseudouridine in mRNA makes the message non-immunogenic and highly translatable, thus offering therapeutic opportunities in medical applications (9).Although the exact mechanism of isomerization is still not clear (4), the incorporation of C5 of the uracil base into the glycosidic bond is catalyzed by either standalone proteins (referred to as ⌿ synthases) (10, 11) or RNA-protein complexes (referred to as H/ACA box ribonucleoproteins) (12). Following site-specific recognition, the nitrogen-carbon glycosidic bond is cleaved, and uracil is rotated and then reattached to the sugar, forming a carbon-carbon glycosidic bond on the polyribonucleotide (Fig. 1) by Michael addition-like or glycal mechanisms (13).The ⌿ synthases have been initially classified based on the Escherichia coli enzymes RluA, RsuA, TruA, TruB, and TruD (10, 11). A sixth family with members from archaea and eukaryotes but not from bacteria was added after discovery of Pus10 (14). The enzyme active site carries a catalytically essential aspartate, which is the only absolutely conserved residue in all ⌿ synthases (15, 16). Substrate recognition by the ⌿ synthase is usually in the context of the sequence or structure of the target site in RNA. Site specificity also varies depending on the ⌿ synthase. For example, RsuA isomerizes U516 of 16S rRNA (17) exclusively, whereas the universally conserved ⌿55 of the T⌿C loop in all elongator tRNAs is catalyzed by TruB (18). RluA catalyzes modification of two distinct RNAs, 23S rRNA (position 746) and some tRNAs (position 32) (19). Member...

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

“…The archaeal Pus10 protein (MJ0041) generates ⌿54 and ⌿55 in archaeal tRNAs (58), although pseudouridine at position 55 can also be generated through an H/ACA guide RNA mechanism (59-62). As no pseudouridine-specific mapping was performed (63,64), the localization of this modification to positions 54 and 55 of specific tRNAs is expected but not verified here. The DUF358 SPOUT-methyltransferase MJ1640 (renamed TrmY) acts in concert with Pus10 to catalyze the biosynthesis of m 1 ⌿ at position 54 (65)(66)(67).…”

MODOMICS: a database of RNA modification pathways. 2017 update

“…Among new sequences are sets of tRNAs from two bacterial species: Streptomyces griseus and Lactococcus lactis ( 19 , 20 ), 60 and 26 sequences, respectively. As technology and methods improve, well-studied sequences continue to undergo revision ( 21 ). We have also introduced links of human tRNA sequences to MINTbase ( 22 ), which is a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.…”

Pseudouridine-Free Escherichia coli Ribosomes

“…These phenotypes do not have immediately obvious links to ribosome function. Two of the genes deleted in the Δ⌿7 strain, rluA and rluF, encode dual-specificity enzymes responsible for ⌿ modifications in certain tRNAs as well as in rRNA (35,36). Thus, some of the phenotypes of the Δ⌿7 strain, including, perhaps, hypersensitivity to hydroxamates, may be due to altered tRNA functionality rather than to ribosome hypomodification.…”