The Ribosome Modulation Factor (RMF) Binding Site on the 100S Ribosome of Escherichia coli

Yoshida, Hideji; Maki, Yoshitaka; Kato, Harubumi; Fujisawa, Hisao; Izutsu, Kaori; Wada, Chieko; Wada, Akira

doi:10.1093/oxfordjournals.jbchem.a003313

Cited by 79 publications

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“…In stationary-phase bacteria, ribosomes become dimerized, which could represent a way to store them. 83,91 Upon readdition of nutrients, the ribosomes are released from their dimerized state within two minutes. 91 Thus, decreased translation is associated with stationary phase in bacteria.…”

Section: Quiescence In E Colimentioning

confidence: 99%

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et al. 2012

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Ensuring the continuity of life requires that individual cells and entire organisms can survive not only in ideal environments, but also in conditions of scarcity. When conditions are unfavorable for proliferation, many cells have the capacity to enter a nondividing state, sometimes for years, while retaining their ability to reenter the proliferative cell cycle. 1,2 This state of reversible cell cycle arrest, known as quiescence, is common and can be seen in stem cells, eggs and spores. Some quiescent cells are surprisingly hardy: they can survive long periods of nutrient starvation, cold temperatures and even desiccation. Entry into quiescence is often associated with dramatic changes in metabolism, defined as the uptake of nutrients and the use of these nutrients for the synthesis of macromolecules and energy. Indeed, proliferating and quiescent fibroblasts are expected to have very different metabolic requirements. While proliferating cells must devote much of their metabolic capacity to biosynthesis in order to create the material necessary to form a new cell, quiescent cells are relieved of this steep metabolic requirement. Many but not all quiescent cells respond by downregulating the synthesis of proteins *Correspondence to: Hilary Coller; Email: hcoller@princeton.edu Submitted: 02/22/12; Accepted: 02/27/12 http://dx.doi.org/10. 4161/cc.19879 Quiescence is a state of reversible cell cycle arrest that can grant protection against many environmental insults. in some systems, cellular quiescence is associated with a low metabolic state characterized by a decrease in glucose uptake and glycolysis, reduced translation rates and activation of autophagy as a means to provide nutrients for survival. For cells in multiple different quiescence model systems, including Saccharomyces cerevisiae, mammalian lymphocytes and hematopoietic stem cells, the Pi3Kinase/TOr signaling pathway helps to integrate information about nutrient availability with cell growth rates. Quiescence signals often inactivate the TOr kinase, resulting in reduced cell growth and biosynthesis. However, quiescence is not always associated with reduced metabolism; it is also possible to achieve a state of cellular quiescence in which glucose uptake, glycolysis and flux through central carbon metabolism are not reduced. in this review, we compare and contrast the metabolic changes that occur with quiescence in different model systems. 2 The signals for quiescence vary for different types of cells. Bacteria and yeast can enter stationary phase, a condition in which they cease cell growth and proliferation, in response to depletion of the glucose in their culture medium or in response to deprivation for a specific nutrient. In mammals, the proliferative state of individual cells is regulated by a host of factors that include not only the presence or absence of nutrients, but also cues from proliferative signaling molecules such as mitogens and situational cues. Quiescent T lymphocytes respond to stimulation of their T-cell receptor with the approp...

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Section: Quiescence In E Colimentioning

confidence: 99%

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et al. 2012

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“…RMF associates 70S ribosomes to convert them to a dimeric form, 100S ribosomes, which is a storage form of ribosome with no translation activity (Wada et al, 1990). RMF binds the peptidyl transferase center or the P site to inhibit reversibly the translation activity of ribosomes (Yoshida et al, 2002(Yoshida et al, , 2004. YfiA and YhbH associates 70S and 100S ribosomes, respectively (Maki et al, 2000).…”

Section: Proteomics Study Of the Ecoli Ribosomes Using Rfhr 2-d Gel mentioning

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.

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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.

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“…In a recent study, it was demonstrated that RMF covers the peptidyl transferase center and the entrance of the peptide exit tunnel (42). The dimerization reaction is reversible, as the 100S ribosomes dissociate back into 70S ribosomes within 2 min after cells are transferred into fresh medium (36,41) and as protein synthesis and cell proliferation resume within 6 min (38).…”

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Modulation of mRNA Stability Participates in Stationary-Phase-Specific Expression of Ribosome Modulation Factor

et al. 2005

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The expression of ribosome modulation factor (RMF) is induced during stationary phase in Escherichia coli. RMF participates in the dimerization of 70S ribosomes to form the 100S ribosome, which is the translationally inactive form of the ribosome. To elucidate the involvement of the control of mRNA stability in growth-phasespecific rmf expression, we investigated rmf mRNA stability in stationary-phase cells and cells inoculated into fresh medium. The rmf mRNA was found to have an extremely long half-life during stationary phase, whereas destabilization of this mRNA took place after the culture was inoculated into fresh medium. RMF and 100S ribosomes disappeared from cells 1 min after inoculation. In addition to control by ppGpp-dependent transcription, these results indicate that the modulation of rmf mRNA stability is also involved in the regulation of growth-phase-specific rmf expression. Unexpectedly, the postinoculation degradation of rmf mRNA was suppressed by the addition of rifampin, suggesting that de novo RNA synthesis is necessary for degradation. This degradation was also suppressed in both a poly(A) polymerase-deficient and an rne-131 mutant strain. We cloned and sequenced the 3-proximal regions of rmf mRNAs and found that most of these 3 ends terminated at the -independent terminator with the addition of a one-to five-A oligo(A) tail in either stationary-phase or inoculated cells. No difference was observed in the length of the poly(A) tail between stationary-phase and inoculated cells. These results suggest that a certain postinoculation-specific regulatory factor participates in the destabilization of rmf mRNA and is dependent on polyadenylation.Bacteria have evolved various mechanisms by which they alter gene expression to adapt to changes in environmental and intracellular conditions. The mechanisms through which different genes modulate their expression depend on their respective functions. In some cases, several different mechanisms, such as the control of transcription and translation and the modulation of the stability of the mRNA and protein, are used to regulate the expression of a single gene.Expression of the ribosome modulation factor (RMF) is induced during stationary phase in the presence of ppGpp, which is known to be a mediator of stringent control (17,36,37). RMF binds to the 50S ribosomal subunit to mediate the dimerization of 70S ribosomes to form the 100S ribosome, which is a translationally inactive form (37). In a recent study, it was demonstrated that RMF covers the peptidyl transferase center and the entrance of the peptide exit tunnel (42). The dimerization reaction is reversible, as the 100S ribosomes dissociate back into 70S ribosomes within 2 min after cells are transferred into fresh medium (36, 41) and as protein synthesis and cell proliferation resume within 6 min (38).Recently, we found that the rmf mRNA is extremely stable in stationary-phase cells. In light of the RMF function described above, it is reasonable to assume that the modulation of rmf mRNA stability pla...

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The Ribosome Modulation Factor (RMF) Binding Site on the 100S Ribosome of Escherichia coli

Cited by 79 publications

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

Modulation of mRNA Stability Participates in Stationary-Phase-Specific Expression of Ribosome Modulation Factor

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