Liberation of Zinc-Containing L31 (RpmE) from Ribosomes by Its Paralogous Gene Product, YtiA, in<i>Bacillus subtilis</i>

Akanuma, Genki; Nanamiya, Hideaki; Natori, Yousuke; Nomura, Naofumi; Kawamura, Fujio

doi:10.1128/jb.188.7.2715-2720.2006

Cited by 77 publications

(102 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…62) Further in vivo and in vitro studies indicated that (i) RpmE is de-stabilized by overexpression of ytiA, (ii) YtiA is incorporated into the ribosome more efficiently than RpmE, and (iii) YtiA can be incorporated into at least a portion of the ribosomes that contain RpmE and incorporation of YtiA results in the liberation of RpmE. 67) From these results, a model for the switching between the two types of L31 was proposed (Fig. 2).…”

Section: Mechanisms Of Switching Between the Two Types Of L31 Proteinmentioning

confidence: 99%

“…2). 60,62,67) During exponential growth in CSM, which is considered to constitute zinc-sufficient conditions, RpmE contains a zinc ion bound to the CxxC motif and thus is stable. In addition, active Zur protein binds to a motif in the promoter of ytiA, the so-called ''Zur box,'' which is highly conserved among the genes regulated by Zur, 65) and thus represses the expression of ytiA.…”

Section: Mechanisms Of Switching Between the Two Types Of L31 Proteinmentioning

confidence: 99%

See 1 more Smart Citation

Towards an Elucidation of the Roles of the Ribosome during Different Growth Phases inBacillus subtilis

Nanamiya

Kawamura

2010

Bioscience, Biotechnology, and Biochemistry

Self Cite

View full text Add to dashboard Cite

Section: Mechanisms Of Switching Between the Two Types Of L31 Proteinmentioning

confidence: 99%

Section: Mechanisms Of Switching Between the Two Types Of L31 Proteinmentioning

confidence: 99%

Towards an Elucidation of the Roles of the Ribosome during Different Growth Phases inBacillus subtilis

Nanamiya

Kawamura

2010

Bioscience, Biotechnology, and Biochemistry

Self Cite

View full text Add to dashboard Cite

“…Panina et al (2003) do not explain how CϪ forms replace Cϩ forms in ribosomes. We have recently found that when YtiA is added to RpmE-containing ribosome fractions, YtiA-containing ribosomes are detected, suggesting that the affinity of YtiA to ribosomes is higher than that of RpmE and thus newly synthesized YtiA can liberate RpmE from ribosomes (Akanuma et al, 2006). Zinc is an essential trace metal ion for all living cells, which is required for catalytic activity of enzymes and also for structural folding in protein-protein and protein-DNA interactions (Berg and Shi, 1996).…”

Section: Duplication Of R-protein Genes and The Zinc Homeostasismentioning

confidence: 99%

Proteomic study of the Bacillus subtilis ribosome: Finding of zinc-dependent replacement for ribosomal protein L31 paralogues

Nanamiya

Kawamura

Kosono

2006

J. Gen. Appl. Microbiol.

Self Cite

View full text Add to dashboard Cite

The ribosome is a universal molecular machinery of translation comprising three kinds of ribosomal RNA (rRNA) and many ribosomal proteins (r-proteins). The functional domains of the ribosome, which are involved in the decoding of genetic information in messenger RNA and formation of peptide bonds, consist entirely of rRNAs (reviewed in Ramakrishnan, 2002). As rRNAs are subjected to strong selective pressure and are highly conserved, they have been used as a reference molecule in phylogeny. In contrast, r-proteins show more diversity in their sequences and composition, compared to rRNAs.Recent development of genomics and proteomics has enabled an examination of r-protein genes in prokaryotic, eukaryotic and organelle genomes. A recent comprehensive study of ribosomal genes in completed genomes revealed 57 r-protein families in the bacterial domain, 68 in the archaeal domain and 78 in the eukaryotic domain (Lecompte et al., 2002 Recent advanced studies of genomics and proteomics have revealed the variation and diversity of ribosomal proteins (r-proteins) in different organisms and organelles. Radical free and highly reducing (RFHR) two-dimensional (2-D) electrophoresis is known to be powerful for separating ribosomal proteins that are usually small and basic, and not separated well by standard 2-D electrophoresis. Using the RFHR method, we investigated the protein profile of the Bacillus subtilis ribosomes by a proteomic approach. We found that two L31 paralogue proteins (RpmE and YtiA) showed different temporal expression patterns in the ribosomes. The RpmE protein, which is an L31 variant with a Zn-binding motif, binds one zinc ion at the motif, which is required for stabilization of the protein in the cell. On the other hand, the expression of the ytiA gene, which encodes another L31 variant (YtiA) without the Zn-binding motif, is negatively controlled by the zinc-specific transcriptional repressor Zur and is likely induced by zinc starvation. This article reviews the recent findings that replacement of two types of L31 proteins in the ribosome is controlled by the intracellular zinc concentration.

show abstract

“…8b). The low occupancy of L31 can be explained by its flexible binding mode, which may also be important for the function of L31 as a Zn 21 reservoir for the cell 28 .…”

mentioning

confidence: 99%

Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM

Fischer

Neumann

Konevega

et al. 2015

Nature

364

443

View full text Add to dashboard Cite

Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution 1,2 and all structures available to date have been limited to resolutions above 3 Å 3,4 . Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (C s )-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome 5 (2.8 Å ), but provides more detailed information (2.65 Å ) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.Determining the structure of large, dynamic biological macromolecules at a uniformly high resolution provides a challenge both for X-ray crystallography and cryo-EM. Here we have used aberration-corrected cryo-EM in combination with extensive computational sorting to solve *These authors contributed equally to this work.

show abstract

Liberation of Zinc-Containing L31 (RpmE) from Ribosomes by Its Paralogous Gene Product, YtiA, inBacillus subtilis

Cited by 77 publications

References 21 publications

Towards an Elucidation of the Roles of the Ribosome during Different Growth Phases inBacillus subtilis

Towards an Elucidation of the Roles of the Ribosome during Different Growth Phases inBacillus subtilis

Proteomic study of the Bacillus subtilis ribosome: Finding of zinc-dependent replacement for ribosomal protein L31 paralogues

Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM

Contact Info

Product

Resources

About