Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase <i>Escherichia coli</i>

Maki, Yoshitaka; Yoshida, Hideji; Wada, Akira

doi:10.1046/j.1365-2443.2000.00389.x

Cited by 141 publications

(211 citation statements)

References 32 publications

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“…Standard NMR samples were prepared containing approximately 1-2 mM pY protein in gel-filtration buffer supplemented with 0.3 mM NaN 3 …”

Section: Sample Preparationmentioning

confidence: 99%

“…Qualitative 3 J HNHa coupling constants were measured from an HNHA [15] experiment using a correction factor of 0.9 to compensate the different relaxation properties of the diagonal and cross peaks. 3 J HNHa values were directly used in structural refinement [16]. Additionally, dihedral angle constraints of )65(±25)°and )120(±30)°for / were set for 3 J HNHa <5.8 Hz and >8.0 Hz, respectively.…”

Section: Nmr Spectroscopymentioning

confidence: 99%

“…A stretch of six aspartates and glutamates is also present in the unstructured C-terminus of the protein. The unstructured region of pY (C-terminal residues 91-112) does not appear to be important for binding to ribosomes, as E. coli protein YhbH, a homolog of pY, which lacks the 18 C-terminal amino acids, binds equally well to ribosomal subunits [3].…”

Section: Role Of Conserved Residuesmentioning

confidence: 99%

“…pY shows about 40% identity with the protein encoded by E. coli yhbH gene. The association of pY and 70S ribosomes contrasts with the preferential binding of YhbH and the dimerized 100S ribosomes in the stationary phase of cell growth [3]. The authors suggested that these related proteins play a stabilization role during ribosome storage.…”

mentioning

confidence: 99%

“…Protein Y, the product of yfiA gene, is a ribosome-associated protein present in E. coli and many other bacteria [1][2][3]. pY was earlier assigned to the r 54 modulation protein family based on the observation that mutations in the related downstream r 54 gene cause an increase in the level of expression from r 54 -dependent promoters [4].pY (also called ribosome associated inhibitor, RaiA) [2] was detected in the ribosome fraction during environmental stress, as a consequence of either low temperature [2] or excessive cell density [2,3]. Furthermore, pY binds to the small ribosomal subunit in an Mg 2+ -dependent manner and becomes less exposed to solvent upon association of the small and large ribosomal subunits.…”

mentioning

confidence: 99%

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Ribosome‐associated factor Y adopts a fold resembling a double‐stranded RNA binding domain scaffold

Ye¹,

Serganov²,

Hu³

et al. 2002

European Journal of Biochemistry

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Escherichia coli protein Y (pY) binds to the small ribosomal subunit and stabilizes ribosomes against dissociation when bacteria experience environmental stress. pY inhibits translation in vitro, most probably by interfering with the binding of the aminoacyl-tRNA to the ribosomal A site. Such a translational arrest may mediate overall adaptation of cells to environmental conditions. We have determined the 3D solution structure of a 112-residue pY and have studied its backbone dynamic by NMR spectroscopy. The structure has a babbba topology and represents a compact twolayered sandwich of two nearly parallel a helices packed against the same side of a four-stranded b sheet. The 23 C-terminal residues of the protein are disordered. Longrange angular constraints provided by residual dipolar coupling data proved critical for precisely defining the position of helix 1. Our data establish that the C-terminal region of helix 1 and the loop linking this helix with strand b2 show significant conformational exchange in the ms-ls time scale, which may have relevance to the interaction of pY with ribosomal subunits. Distribution of the conserved residues on the protein surface highlights a positively charged region towards the C-terminal segments of both a helices, which most probably constitutes an RNA binding site. The observed babbba topology of pY resembles the abbba topology of double-stranded RNA-binding domains, despite limited sequence similarity. It appears probable that functional properties of pY are not identical to those of dsRBDs, as the postulated RNA-binding site in pY does not coincide with the RNA-binding surface of the dsRBDs.Keywords: backbone dynamics; dsRBD; molecular alignment; residual dipolar couplings; RNA-binding domain.Protein expression is finely tuned in the cell allowing for adaptations to various environmental changes. The regulation strategies adopted by the cell encompass almost every aspect of the protein production process, including mRNA transcription, translation in the ribosome and protein degradation. Ribosome activity constitutes an important target in the control of protein expression. Protein Y, the product of yfiA gene, is a ribosome-associated protein present in E. coli and many other bacteria [1][2][3]. pY was earlier assigned to the r 54 modulation protein family based on the observation that mutations in the related downstream r 54 gene cause an increase in the level of expression from r 54 -dependent promoters [4].pY (also called ribosome associated inhibitor, RaiA) [2] was detected in the ribosome fraction during environmental stress, as a consequence of either low temperature [2] or excessive cell density [2,3]. Furthermore, pY binds to the small ribosomal subunit in an Mg 2+ -dependent manner and becomes less exposed to solvent upon association of the small and large ribosomal subunits. This suggests an intersubunit position for pY in the 70S ribosome and may explain its ribosome stabilization effect [1]. pY inhibits translation most probably by interfering with the binding...

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“…Standard NMR samples were prepared containing approximately 1-2 mM pY protein in gel-filtration buffer supplemented with 0.3 mM NaN 3 …”

Section: Sample Preparationmentioning

confidence: 99%

Section: Nmr Spectroscopymentioning

confidence: 99%

Section: Role Of Conserved Residuesmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Ribosome‐associated factor Y adopts a fold resembling a double‐stranded RNA binding domain scaffold

Ye¹,

Serganov²,

Hu³

et al. 2002

European Journal of Biochemistry

View full text Add to dashboard Cite

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Cold Shock Response inEscherichia Coli: a Model System to Study Posttranscriptional Regulation

Giuliodori

2016

Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria

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Consistency of cybernetic variables with gene expression profiles: A more rigorous test

DeVilbiss

Mandli²,

Ramkrishna³

2018

Biotechnology Progress

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Diauxic growth of Escherichia coli is driven by a host of internal, complex regulatory actions. In this classic scenario of cellular control, the cell employs a rational algorithm to modulate its metabolism in a competitive fashion. Cybernetic models of metabolism, whose development now spans three decades, were first formulated to describe regulation of cells in complex, multi-substrate environments. They modeled this scenario using the hypothesis that the formation of the enzymatic machinery is regulated to maximize a return on investment. While this assumption is made on the basis of logical arguments rooted in evolutionary principles, little effort has been taken to validate if enzymes are truly synthesized in the same fashion that is predicted by cybernetic variables. This work revisits the original cybernetic models describing diauxic growth and compares their predictions of enzyme synthesis control with time series gene expression data in microarray and qRT-PCR formats. Three separate studies are made for two different strains of E. coli. The first is for the growth of E. coli BW25113 on a mixture of glucose and acetate, whose gene expression changes are metered by microarray. Another is also for the sequential consumption of glucose and acetate but involves strain MG1655 and employs qRT-PCR. The final is for E. coli MG1655 on glucose and lactose. By demonstrating how cybernetic variables for induced enzyme synthesis mimic the behavior of transcriptional data, a strong argument for using cybernetic models is made. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:858-867, 2018.

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Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli

Cited by 141 publications

References 32 publications

Ribosome‐associated factor Y adopts a fold resembling a double‐stranded RNA binding domain scaffold

Ribosome‐associated factor Y adopts a fold resembling a double‐stranded RNA binding domain scaffold

Cold Shock Response inEscherichia Coli: a Model System to Study Posttranscriptional Regulation

Consistency of cybernetic variables with gene expression profiles: A more rigorous test

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