The Role of RbfA in 16S rRNA Processing and Cell Growth at Low Temperature in Escherichia coli

Xia, Bing; Ke, Haiping; Shinde, Ujwal; Inouye, Masayori

doi:10.1016/s0022-2836(03)00953-7

Cited by 84 publications

(72 citation statements)

References 21 publications

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“…The relative amount of 17S rRNA [17S/(16S + 17S)] was 5.4-fold higher in the rbfA:: Km R mutant STN409 than in the wild-type strain MW100 (Fig. 5) in agreement with previous findings (Bylund et al 1998;Xia et al 2003). The rpsE mutations did reduce the relative amount of 17S rRNA but the effect was rather small, 1.1-to 1.2-fold (Fig.…”

Section: Overexpression Of Rimp In the Absence Of Rbfa Causes Synthetsupporting

confidence: 91%

“…The rpsE mutations increase the proportion of 30S subunits that take part in translation A strain that lacks RbfA is deficient in the maturation of the 30S ribosomal subunits and shows an accumulation of free 50S and 30S ribosomal subunits and much less translating ribosomes than a wild-type strain probably as a result of this maturation deficiency (Dammel and Noller 1995;Bylund et al 1998;Inoue et al 2003;Xia et al 2003). Polysome profiles obtained after centrifugation through sucrose gradients of total cell extracts of relevant strains grown at 30°C confirmed this observation.…”

Section: Overexpression Of Rimp In the Absence Of Rbfa Causes Synthetmentioning

confidence: 84%

“…Mutations in both 16S rRNA and rbfA affect ribosome function and biogenesis in similar ways, with increased levels of free 50S and 30S subunits and decreased levels of 70S ribosomes and polysomes Noller 1993, 1995). An rbfA null mutant also showed slowed conversion of 17S rRNA to mature 16S rRNA (Bylund et al 1998), which was exacerbated at lower temperatures (Xia et al 2003). All of these phenotypes are shared by mutants lacking the 30S ribosomal subunit biogenesis factors Era (Nashimoto et al 1985), KsgA (Connolly et al 2008), RimM (Lövgren et al 2004), RimP (Nord et al 2009), and YjeQ/RsgA (Guo et al 2011).…”

Section: Introductionmentioning

confidence: 99%

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Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor

Nord

Bhatt

Tükenmez

et al. 2015

RNA

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The in vivo assembly of ribosomal subunits requires assistance by maturation proteins that are not part of mature ribosomes. One such protein, RbfA, associates with the 30S ribosomal subunits. Loss of RbfA causes cold sensitivity and defects of the 30S subunit biogenesis and its overexpression partially suppresses the dominant cold sensitivity caused by a C23U mutation in the central pseudoknot of 16S rRNA, a structure essential for ribosome function. We have isolated suppressor mutations that restore partially the growth of an RbfA-lacking strain. Most of the strongest suppressor mutations alter one out of three distinct positions in the carboxy-terminal domain of ribosomal protein S5 (S5) in direct contact with helix 1 and helix 2 of the central pseudoknot. Their effect is to increase the translational capacity of the RbfA-lacking strain as evidenced by an increase in polysomes in the suppressed strains. Overexpression of RimP, a protein factor that along with RbfA regulates formation of the ribosome's central pseudoknot, was lethal to the RbfA-lacking strain but not to a wild-type strain and this lethality was suppressed by the alterations in S5. The S5 mutants alter translational fidelity but these changes do not explain consistently their effect on the RbfA-lacking strain. Our genetic results support a role for the region of S5 modified in the suppressors in the formation of the central pseudoknot in 16S rRNA.

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Section: Overexpression Of Rimp In the Absence Of Rbfa Causes Synthetsupporting

confidence: 91%

Section: Overexpression Of Rimp In the Absence Of Rbfa Causes Synthetmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor

Nord

Bhatt

Tükenmez

et al. 2015

RNA

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“…Cells lacking RimM or RbfA or cells depleted for Era accumulate 17S rRNA (Bylund et al 1998;Inoue et al 2003;Xia et al 2003), and the levels of polysomes decrease with a concomitant increase in free 30S and 50S subunits (this paper; Dammel and Noller 1995;Inoue et al 2003). Thus, these three proteins seem to take part in late steps of the maturation of the 30S subunits that precede the conversion of 17S to 16S rRNA.…”

Section: Rimm-yy→aa-dependent and Rimm-yy→aa-independent Suppressionmentioning

confidence: 74%

The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits

Lövgren

Bylund²,

Srivastava³

et al. 2004

RNA

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The RimM protein in Escherichia coli is associated with free 30S ribosomal subunits but not with 70S ribosomes. A ⌬rimM mutant is defective in 30S maturation and accumulates 17S rRNA. To study the interaction of RimM with the 30S and its involvement in 30S maturation, RimM amino acid substitution mutants were constructed. A mutant RimM (RimM-YY→AA), containing alanine substitutions for two adjacent tyrosines within the PRC ␤-barrel domain, showed a reduced binding to 30S and an accumulation of 17S rRNA compared to wild-type RimM. The (RimM-YY→AA) and ⌬rimM mutants had significantly lower amounts of polysomes and also reduced levels of 30S relative to 50S compared to a wild-type strain. A mutation in rpsS, which encodes r-protein S19, suppressed the polysome-and 16S rRNA processing deficiencies of the RimM-YY→AA but not that of the ⌬rimM mutant. A mutation in rpsM, which encodes r-protein S13, suppressed the polysome deficiency of both rimM mutants. Suppressor mutations, found in either helices 31 or 33b of 16S rRNA, improved growth of both the RimM-YY→AA and ⌬rimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY→AA mutant more efficiently than that of the ⌬rimM mutant. Helices 31 and 33b are known to interact with S13 and S19, respectively, and S13 is known to interact with S19. A GST-RimM but not a GST-RimM(YY→AA) protein bound strongly to S19 in 30S. Thus, RimM likely facilitates maturation of the region of the head of 30S that contains S13 and S19 as well as helices 31 and 33b.

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“…This lability almost certainly involves helices 44 and 45 and is consistent with the drop-off in ArmA activity at very high [Mg +2 ], where hyper-stabilization of the 30S subunit structure may be hindering the conformation change needed for ArmA to bind. Structural support for a significant conformation change in the helix 44/45 region comes from cryo-EM studies of the complex of RbfA with the 30S ribosomal subunits (Bylund et al 1998;Xia et al 2003).…”

Section: Discussionmentioning

confidence: 99%

The aminoglycoside resistance methyltransferases from the ArmA/Rmt family operate late in the 30S ribosomal biogenesis pathway

Zarubica¹,

Baker²,

Wright³

et al. 2010

RNA

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Bacterial resistance to 4,6-type aminoglycoside antibiotics, which target the ribosome, has been traced to the ArmA/RmtA family of rRNA methyltransferases. These plasmid-encoded enzymes transfer a methyl group from S-adenosyl-L-methionine to N7 of the buried G1405 in the aminoglycoside binding site of 16S rRNA of the 30S ribosomal subunit. ArmA methylates mature 30S subunits but not 16S rRNA, 50S, or 70S ribosomal subunits or isolated Helix 44 of the 30S subunit. To more fully characterize this family of enzymes, we have investigated the substrate requirements of ArmA and to a lesser extent its ortholog RmtA. We determined the Mg +2 dependence of ArmA activity toward the 30S ribosomal subunits and found that the enzyme recognizes both low Mg +2 (translationally inactive) and high Mg +2 (translationally active) forms of this substrate. We tested the effects of LiCl pretreatment of the 30S subunits, initiation factor 3 (IF3), and gentamicin/kasugamycin resistance methyltransferase (KsgA) on ArmA activity and determined whether in vivo derived pre-30S ribosomal subunits are ArmA methylation substrates. ArmA failed to methylate the 30S subunits generated from LiCl washes above 0.75 M, despite the apparent retention of ribosomal proteins and a fully mature 16S rRNA. From our experiments, we conclude that ArmA is most active toward the 30S ribosomal subunits that are at or very near full maturity, but that it can also recognize more than one form of the 30S subunit.

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The Role of RbfA in 16S rRNA Processing and Cell Growth at Low Temperature in Escherichia coli

Cited by 84 publications

References 21 publications

Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor

Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor

The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits

The aminoglycoside resistance methyltransferases from the ArmA/Rmt family operate late in the 30S ribosomal biogenesis pathway

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