Modifications of ribosomal RNA: From enzymes to function

Сергиев, Петр В.; Golovina, Anna Y.; Prokhorova, I.; Sergeeva, Olga V.; Osterman, Ilya А.; Nesterchuk, Mikhail V.; Burakovsky, Dmitry E.; Bøgdanov, A.; Dontsova, Olga А.

doi:10.1007/978-3-7091-0215-2_9

Cited by 40 publications

(60 citation statements)

References 128 publications

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“…On the basis of this observation, the 45S particle has been regarded as a dead-end or breakdown product of the 50S subunit (21). However, in this study, we demonstrated that the 45S particle could actually be converted to the 50S subunit in ΔrlmE (Fig.…”

Section: Discussionmentioning

confidence: 59%

“…The 45S particle of the ΔrlmE strain has been speculated to be a dead end or breakdown product, rather than a bona fide precursor, of the 50S subunit (21). To investigate whether the 45S particle in ΔrlmE is an authentic precursor of the 50S subunit, we cultured the E. coli ΔrlmE strain in the presence of [ 13 C] adenosine (Ado), to label rRNAs with 13 C-Ado, and then cultured the cells for several hours in LB medium with nonlabeled Ado.…”

Section: Resultsmentioning

confidence: 99%

“…1C) (15) or ObgE (16). It remains unknown, however, whether this 45S particle is able to form an active 50S subunit (21). The cold-sensitive phenotype, along with accumulation of the 45S particle, was alleviated by overexpression of the obgE or engA GTPase (22), indicating that RlmE is an assembly factor that acts at a late step of 50S formation.…”

Section: Significancementioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 59%

Section: Resultsmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

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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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“…In the rRNA of Escherichia coli, 36 modified nucleotides are represented by 10 pseudouridines, one dihydrouridine, and one unknown modification, while the rest of the 24 modified nucleotides are methylated ones (Sergiev et al 2011). After the introduction of a convenient gene inactivation method based on the lambda Red system (Datsenko and Wanner 2000), a comprehensive collection of E. coli gene knockout strains was created (Baba et al 2006).…”

Section: Introductionmentioning

confidence: 99%

The last rRNA methyltransferase of E. coli revealed: The yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA

Golovina

Dzama

Osterman

et al. 2012

RNA

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The ribosomal RNA (rRNA) of Escherichia coli contains 24 methylated residues. A set of 22 methyltransferases responsible for modification of 23 residues has been described previously. Herein we report the identification of the yhiR gene as encoding the enzyme that modifies the 23S rRNA nucleotide A2030, the last methylated rRNA nucleotide whose modification enzyme was not known. YhiR prefers protein-free 23S rRNA to ribonucleoprotein particles containing only part of the 50S subunit proteins and does not methylate the assembled 50S subunit. We suggest renaming the yhiR gene to rlmJ according to the rRNA methyltransferase nomenclature. The phenotype of yhiR knockout gene is very mild under various growth conditions and at the stationary phase, except for a small growth advantage at anaerobic conditions. Only minor changes in the total E. coli proteome could be observed in a cell devoid of the 23S rRNA nucleotide A2030 methylation.

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“…Complexity of an organism correlates with the number of modified residues in rRNA (Decatur and Fournier 2002). The majority of modified nucleotides in Escherichia coli rRNA are various types of base and ribose methylated residues (Sergiev et al 2011a). Methyltransferases modify rRNA at certain stages of the assembly.…”

Section: Introductionmentioning

confidence: 99%

Properties of small rRNA methyltransferase RsmD: Mutational and kinetic study

Sergeeva

Prokhorova²,

Ordabaev³

et al. 2012

RNA

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Ribosomal RNA modification is accomplished by a variety of enzymes acting on all stages of ribosome assembly. Among rRNA methyltransferases of Escherichia coli, RsmD deserves special attention. Despite its minimalistic domain architecture, it is able to recognize a single target nucleotide G966 of the 16S rRNA. RsmD acts late in the assembly process and is able to modify a completely assembled 30S subunit. Here, we show that it possesses superior binding properties toward the unmodified 30S subunit but is unable to bind a 30S subunit modified at G966. RsmD is unusual in its ability to withstand multiple amino acid substitutions of the active site. Such efficiency of RsmD may be useful to complete the modification of a 30S subunit ahead of the 30S subunit's involvement in translation.

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Modifications of ribosomal RNA: From enzymes to function

Cited by 40 publications

References 128 publications

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

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

The last rRNA methyltransferase of E. coli revealed: The yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA

Properties of small rRNA methyltransferase RsmD: Mutational and kinetic study

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