Identification of pseudouridine methyltransferase in <i>Escherichia coli</i>

Ero, Rya; Peil, Lauri; Liiv, Aivar; Rèmme, Jaanus

doi:10.1261/rna.1186608

Cited by 56 publications

(72 citation statements)

References 70 publications

(94 reference statements)

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“…As the preferred substrate for RluD is the assembled 50S subunit (Leppik et al 2007;Vaidyanathan et al 2007), YbeA would methylate C1915 at the same or a later stage of ribosome maturation. Consistent with this, the accompanying article (Ero et al 2008) shows that YbeA activity requires prior conversion of nucleotide 1915 to pseudouridine and for C1915 to be presented within the context of the 70S ribosome.…”

Section: Sequence Analysis Of Ybea Orthologsmentioning

confidence: 53%

YbeA is the m³Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

Purta¹,

Kamińska²,

Kasprzak³

et al. 2008

RNA

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Pseudouridines in the stable RNAs of Bacteria are seldom subjected to further modification. There are 11 pseudouridine (C) sites in Escherichia coli rRNA, and further modification is found only at C1915 in 23S rRNA, where the N-3 position of the base becomes methylated. Here, we report the identity of the E. coli methyltransferase that specifically catalyzes methyl group addition to form m 3 C1915. Analyses of E. coli rRNAs using MALDI mass spectrometry showed that inactivation of the ybeA gene leads to loss of methylation at nucleotide C1915. Methylation is restored by complementing the knockout strain with a plasmid-encoded copy of ybeA. Homologs of the ybeA gene, and thus presumably the ensuing methylation at nucleotide m 3 C1915, are present in most bacterial lineages but are essentially absent in the Archaea and Eukaryota. Loss of ybeA function in E. coli causes a slight slowing of the growth rate. Phylogenetically, ybeA and its homologs are grouped with other putative S-adenosylmethionine-dependent, SPOUT methyltransferase genes in the Cluster of Orthologous Genes COG1576; ybeA is the first member to be functionally characterized. The YbeA methyltransferase is active as a homodimer and docks comfortably into the ribosomal A site without encroaching into the P site. YbeA makes extensive interface contacts with both the 30S and 50S subunits to align its active site cofactor adjacent to nucleotide C1915. Methylation by YbeA (redesignated RlmH for rRNA large subunit methyltransferase H) possibly functions as a stamp of approval signifying that the 50S subunit has engaged in translational initiation.

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Section: Sequence Analysis Of Ybea Orthologsmentioning

confidence: 53%

YbeA is the m³Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

Purta¹,

Kamińska²,

Kasprzak³

et al. 2008

RNA

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“…The RlmH methyltransferase, which is responsible for 3-methylpseudouridine (m 3 Ψ) formation at position 1915 (m 3 Ψ) in 23S rRNA, employs 70S ribosome as a substrate (23). Therefore, if the 45S particle of ΔrlmE were a breakdown product of mature 50S subunits, m 3 Ψ1915 would be present in 23S rRNA of the 45S particle.…”

Section: Resultsmentioning

confidence: 99%

Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly

Arai

Ishiguro

Kimura

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Ribosome biogenesis requires multiple assembly factors. In Escherichia coli, deletion of RlmE, the methyltransferase responsible for the 2′-O-methyluridine modification at position 2552 (Um2552) in helix 92 of the 23S rRNA, results in slow growth and accumulation of the 45S particle. We demonstrate that the 45S particle that accumulates in ΔrlmE is a genuine precursor that can be assembled into the 50S subunit. Indeed, 50S formation from the 45S precursor could be promoted by RlmE-mediated Um2552 formation in vitro. Ribosomal protein L36 (encoded by rpmJ) was completely absent from the 45S precursor in ΔrlmE, and we observed a strong genetic interaction between rlmE and rpmJ. Structural probing of 23S rRNA and high-salt stripping of 45S components revealed that RlmE-mediated methylation promotes interdomain interactions via the association between helices 92 and 71, stabilized by the single 2′-O-methylation of Um2552, in concert with the incorporation of L36, triggering late steps of 50S subunit assembly.R ibosomes are essential ribonucleoprotein complexes that translate the genetic information encoded by mRNA into protein. Intact bacterial ribosomes, which have a sedimentation coefficient of 70S, consist of large (50S) and small (30S) subunits. Each subunit can be reconstituted in vitro from its individual component ribosomal RNAs and proteins (1-5), indicating that these components contain all of the information necessary to automatically assemble into functional subunits. Because the intermediate particles observed in an in vitro reconstitution of the subunits are similar to those observed in vivo, assembly maps that describe the order of ribosomal protein binding in vitro are useful tools for understanding ribosome biogenesis in the cell (6). However, assembly is slower in vitro than in vivo, and nonphysiological conditions, such as high-salt concentration and high temperature, are required for in vitro assembly.In the cell, ribosome assembly is coordinated with the transcription and processing of large precursor rRNAs encoded by the rrn operon (3, 7). Once transcription starts, nascent transcripts rapidly form local secondary and tertiary structures that serve as binding sites for the primary ribosomal proteins, thereby initiating ribosome assembly. However, hierarchical assembly starting at the 5′-terminal domains of the 16S and 23S rRNAs is not essential for ribosome formation in the cell (8) because nonribosomal factors, termed "assembly factors," facilitate rapid and efficient assembly of ribosomal particles. Ribosome biogenesis is an energy-consuming process in which a number of assembly factors, including RNA helicases, GTPases, protein chaperones, and rRNA-modifying enzymes, support efficient assembly of each subunit (6, 9, 10). Individual mutation or deletion of several assembly factors causes accumulation of immature 50S subunits that sediment at 40S or 45S. For example, the RNA helicase SrmB participates in the early stage of 50S assembly (11,12); deletion of srmB results in accumulation of a 40S ...

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“…The knotted proteins YibK from Haemophilus influenzae and YbeA from Escherichia coli are single-domain, homodimeric methyltransferases (MTases), whose structures, enzymatic functions, and folding pathways have been probed using a combination of biophysical, biochemical, and computational techniques (18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Both proteins adopt an α/β-fold and contain a righthanded trefoil knot, where at least 40 amino acid residues have passed through a similarly sized loop ( Fig.…”

mentioning

confidence: 99%

Experimental detection of knotted conformations in denatured proteins

Mallam

Rogers

Jackson

2010

Proc. Natl. Acad. Sci. U.S.A.

120

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Structures that contain a knot formed by the path of the polypeptide backbone represent some of the most complex topologies observed in proteins. How or why these topological knots arise remains unclear. By developing a method to experimentally trap and detect knots in nonnative polypeptide chains, we find that two knotted methyltransferases, YibK and YbeA, can exist in a trefoil-knot conformation even in their chemically unfolded states. The unique denatured-state topology of these molecules explains their ability to efficiently fold to their native knotted structures in vitro and offers insights into the potential role of knots in proteins. Furthermore, the high prevalence of the denatured-state knots identified here suggests that they are either difficult to untie or that threading of any untied molecules is rapid and spontaneous. The occurrence of such knotted topologies in unfolded polypeptide chains raises the possibility that they could play an important, and as yet unexplored, role in folding and misfolding processes in vivo.

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Identification of pseudouridine methyltransferase in Escherichia coli

Cited by 56 publications

References 70 publications

YbeA is the m³Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

YbeA is the m³Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly

Experimental detection of knotted conformations in denatured proteins

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Identification of pseudouridine methyltransferase in Escherichia coli

Cited by 56 publications

References 70 publications

YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly

Experimental detection of knotted conformations in denatured proteins

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YbeA is the m³Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

YbeA is the m³Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA