What do we know about ribosomal RNA methylation in Escherichia coli?

Sergeeva, Olga V.; Bøgdanov, A.; Сергиев, Петр В.

doi:10.1016/j.biochi.2014.11.019

Cited by 78 publications

(93 citation statements)

References 80 publications

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“…Ribosomal RNA (rRNA) is modified primarily near key functional sites, including the decoding center responsible for accurate translation of messenger RNA into protein 4, 5 . In bacteria, uridine 1915 of the 23S rRNA undergoes two steps of post-transcriptional modification—pseudouridylation, followed by N3-methylation—that convert it to 3-methylpseudouridine (m 3 Ψ).…”

Section: Introductionmentioning

confidence: 99%

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine

Koh

Madireddy

Beane

et al. 2017

Sci Rep

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Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site. One monomer provides the SAM-binding site, whereas the conserved C-terminal tail of the second monomer provides residues essential for catalysis. Our findings elucidate the mechanism by which a small protein dimer assembles a functionally asymmetric architecture.

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Section: Introductionmentioning

confidence: 99%

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine

Koh

Madireddy

Beane

et al. 2017

Sci Rep

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“…In eukaryotes, nucleotide methylations regulate a wide range of fundamental cellular processes, and mutations in these methylating enzymes have been associated with human diseases, including cancer and neurological disorders [15,16,17*,18–31]. In prokaryotes, many rRNA and tRNA methylations are not essential, and not a single rRNA methylation is critical for cell survival [32*]. Consequently, loss-of-function mutations in RNA methylating enzymes are common and under specific conditions beneficial.…”

Section: Introductionmentioning

confidence: 99%

Mutations in RNA methylating enzymes in disease

Stojković

Fujimori

2017

Current Opinion in Chemical Biology

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RNA methylation is an abundant modification identified in various RNA species in both prokaryotic and eukaryotic organisms. However, the functional roles for the majority of these methylations remain largely unclear. In eukaryotes, many RNA methylations have been suggested to participate in fundamental cellular processes. Mutations in eukaryotic RNA methylating enzymes, and a consequent change in methylation, often lead to the development of diseases and disorders. In contrast, loss of RNA methylation in prokaryotes can be beneficial to microorganisms, especially under antibiotic pressure. Here we discuss several recent advances in understanding mutational landscape of both eukaryotic and prokaryotic RNA methylating enzymes and their relevance to disease and antibiotic resistance.

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“…These modifications are chemically diverse and are comprised of methylation, hydroxylation, acetylation, deamination, isomerization, selenylation, reduction, and cyclization, to name a few (Agris, 1996). From this wide variety of modifications, methylation of nucleotides, both at nucleobases and at the ribose moiety, are one of the most common and simplest modifications, and the most prevalent modification in rRNA (Sergeeva, Bogdanov, & Sergiev, 2014). Most of the methylation sites are located in the functional centers of the ribosome: in the decoding and peptidyl transferase centers, as well as on the interface of ribosomal subunits.…”

Section: Introductionmentioning

confidence: 99%

“…The roles of such modifications are not completely understood; however, their conservation across bacterial species implies their functional importance. It is believed that their roles span from structural stabilization of substrate RNA to modulation of the function of the ribosome (e.g., maintenance of translational fidelity) (Li & Mason, 2014; Motorin & Helm, 2011; Sergeeva et al, 2014; Sergiev et al, 2011). Additionally, post-transcriptional modification of rRNA can also confer antibiotic resistance toward ribosome-targeting antibiotics (Leclercq & Courvalin, 1991; Long, Poehlsgaard, Kehrenberg, Schwarz, & Vester, 2006; McCusker & Fujimori, 2012; Poehlsgaard & Douthwaite, 2005; Vester & Long, 2009; Wilson, 2014).…”

Section: Introductionmentioning

confidence: 99%

Radical SAM-Mediated Methylation of Ribosomal RNA

Stojković

Fujimori

2015

Methods in Enzymology

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Post-transcriptional modifications of RNA play an important role in a wide range of biological processes. In ribosomal RNA (rRNA), methylation of nucleotide bases is the predominant modification. In recent years, methylation of adenosine 2503 (A2503) in bacterial 23S rRNA has attracted significant attention due to both the unusual regioselectivity of the methyl group incorporation, as well as the pathophysiological roles of the resultant methylations. Specifically, A2503 is methylated at the C2 and C8 positions of the adenine ring, and the introduced modifications have a profound impact on translational fidelity and antibiotic resistance, respectively. These modifications are performed by RlmN and Cfr, two members, of the recently discovered class of radical S-adenosylmethionine (radical SAM) methylsynthases. Here, we present several methods that can be used to evaluate the activity of these enzymes, under both in vivo and in vitro conditions.

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What do we know about ribosomal RNA methylation in Escherichia coli?

Cited by 78 publications

References 80 publications

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine

Mutations in RNA methylating enzymes in disease

Radical SAM-Mediated Methylation of Ribosomal RNA

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