scholarly journals Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27

2016 ◽  
Vol 198 (13) ◽  
pp. 1857-1867 ◽  
Author(s):  
Rim Maouche ◽  
Hector L. Burgos ◽  
Laetitia My ◽  
Julie P. Viala ◽  
Richard L. Gourse ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Protein ◽  
Transcription Initiation ◽  
Ribosomal Proteins ◽  
Ribosomal Gene ◽  
Small Gtpases ◽  
Ribosomal Protein Genes ◽  
Transcriptional Terminator ◽  
Content Type

ABSTRACTMultiple essential small GTPases are involved in the assembly of the ribosome or in the control of its activity. Among them, ObgE (CgtA) has been shown recently to act as a ribosome antiassociation factor that binds to ppGpp, a regulator whose best-known target is RNA polymerase. The present study was aimed at elucidating the expression ofobgEinEscherichia coli. We show thatobgEis cotranscribed with ribosomal protein genesrplUandrpmAand with a gene of unknown function,yhbE. We show here that about 75% of the transcripts terminate beforeobgE, because there is a transcriptional terminator betweenrpmAandyhbE. As expected for ribosomal protein operons, expression was highest during exponential growth, decreased during entry into stationary phase, and became almost undetectable thereafter. Expression of the operon was derepressed in mutants lacking ppGpp or DksA. However, regulation by these factors appears to occur post-transcription initiation, since no effects of ppGpp and DksA onrplUpromoter activity were observedin vitro.IMPORTANCEThe conserved and essential ObgE GTPase binds to the ribosome and affects its assembly. ObgE has also been reported to impact chromosome segregation, cell division, resistance to DNA damage, and, perhaps most interestingly, persister formation and antibiotic tolerance. However, it is unclear whether these effects are related to its role in ribosome formation. Despite its importance, no studies on ObgE expression have been reported. We demonstrate here thatobgEis expressed from an operon encoding two ribosomal proteins, that the operon's expression varies with the growth phase, and that it is dependent on the transcription regulators ppGpp and DksA. Our results thus demonstrate thatobgEexpression is coupled to ribosomal gene expression.

scholarly journals The yeast omnipotent suppressor SUP46 encodes a ribosomal protein which is a functional and structural homolog of the Escherichia coli S4 ram protein.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 375-386 ◽  
Author(s):  
A Vincent ◽  
S W Liebman
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Protein ◽  
Dna Sequences ◽  
Ribosomal Proteins ◽  
Amino Acid Sequences ◽  
Ribosomal Protein Genes ◽  
Significant Homology ◽  
A Cell ◽  
Functional Equivalent ◽  
Ribosomal Protein S13

Abstract The accurate synthesis of proteins is crucial to the existence of a cell. In yeast, several genes that affect the fidelity of translation have been identified (e.g., omnipotent suppressors, antisuppressors and allosuppressors). We have found that the dominant omnipotent suppressor SUP46 encodes the yeast ribosomal protein S13. S13 is encoded by two similar genes, but only the sup46 copy of the gene is able to fully complement the recessive phenotypes of SUP46 mutations. Both copies of the S13 genes contain introns. Unlike the introns of other duplicated ribosomal protein genes which are highly diverged, the duplicated S13 genes have two nearly identical DNA sequences of 25 and 31 bp in length within their introns. The SUP46 protein has significant homology to the S4 ribosomal protein in prokaryotic-type ribosomes. S4 is encoded by one of the ram (ribosomal ambiguity) genes in Escherichia coli which are the functional equivalent of omnipotent suppressors in yeast. Thus, SUP46 and S4 demonstrate functional as well as sequence conservation between prokaryotic and eukaryotic ribosomal proteins. SUP46 and S4 are most similar in their central amino acid sequences. Interestingly, the alterations resulting from the SUP46 mutations and the segment of the S4 protein involved in binding to the 16S rRNA are within this most conserved region.

The relationship between the spoT gene, the synthesis of stable RNA, ribosomal proteins, and the ββ′ subunits of RNA polymerase following a nutritional shiftup of Escherichia coli

1978 ◽  
Vol 56 (6) ◽  
pp. 528-533 ◽  
Author(s):  
Stephen M. Boyle ◽  
Frederick Chu ◽  
Nathan Brot ◽  
Bruce H. Sells
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Rna Synthesis ◽  
Transient Increase ◽  
Spot Gene ◽  
The Relationship

The level of ppGpp and rates of synthesis of stable RNA, ribosomal protein, and the β and β′ subunits of RNA polymerase were measured following a nutritional shiftup in Escherichia coli strains, NF 929 (spoT+) and NF 930 (spoT'−). In the spoT+ strain, ppGpp levels decreased 50% within 2 min following shiftup, and the rates of synthesis of stable RNA, ribosomal proteins, and the β and β′ subunits of RNA polymerase increased with little or no lag. In contrast, in the spoT− strain, ppGpp levels transiently increased 40% during the first 6 min following shiftup. An inhibition in the rate of stable RNA synthesis and a delay in the increased synthesis of ribosomal proteins and β and β′ subunits occurred concurrently with the transient increase in ppGpp. In addition, the DNA-dependent synthesis in vitro of the β and β′ subunits of RNA polymerase was inhibited by physiological levels of ppGpp. Because of the timing and magnitude of the changes in ppGpp levels in the spoT− strain versus the timing when the new rates of stable RNA, ribosomal protein, and β and β′ subunits synthesis are reached, it is concluded that ppGpp is not the sole element regulating the expression of these genes.

Structure and expression of ribosomal protein genes in Xenopus laevis

1995 ◽  
Vol 73 (11-12) ◽  
pp. 969-977 ◽  
Author(s):  
Francesco Amaldi ◽  
Olga Camacho-Vanegas ◽  
Francesco Cecconi ◽  
Fabrizio Loreni ◽  
Beatrice Cardinali ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Translational Regulation ◽  
Cultured Cells ◽  
Structural Features ◽  
Ribosomal Protein Genes ◽  
Translation Apparatus ◽  
And Function

In Xenopus laevis, as well as in other vertebrates, ribosomal proteins (r-proteins) are coded by a class of genes that share some organizational and structural features. One of these, also common to genes coding for other proteins involved in the translation apparatus synthesis and function, is the presence within their introns of sequences coding for small nucleolar RNAs. Another feature is the presence of common structures, mainly in the regions surrounding the 5′ ends, involved in their coregulated expression. This is attained at various regulatory levels: transcriptional, posttranscriptional, and translational. Particular attention is given here to regulation at the translational level, which has been studied during Xenopus oogenesis and embryogenesis and also during nutritional changes of Xenopus cultured cells. This regulation, which responds to the cellular need for new ribosomes, operates by changing the fraction of rp-mRNA (ribosomal protein mRNA) engaged on polysomes. A typical 5′ untranslated region characterizing all vertebrate rp-mRNAs analyzed to date is responsible for this translational behaviour: it is always short and starts with an 8–12 nucleotide polypyrimidine tract. This region binds in vitro some proteins that can represent putative trans-acting factors for this translational regulation.Key words: ribosomal proteins, snoRNA, translational regulation, Xenopus laevis.

scholarly journals A memory of eS25 loss drives resistance phenotypes

2020 ◽  
Author(s):  
Alex G Johnson ◽  
Ryan A Flynn ◽  
Christopher P Lapointe ◽  
Yaw Shin Ooi ◽  
Michael L Zhao ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Translational Control ◽  
Ribosomal Proteins ◽  
Ribosomal Protein Gene ◽  
Human Cell Line ◽  
Cellular Protein ◽  
Ribosomal Protein Genes ◽  
Genomic Locus ◽  
Cellular Phenotypes

Abstract In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.

scholarly journals A memory of RPS25 loss drives resistance phenotypes

2019 ◽  
Author(s):  
Alex G. Johnson ◽  
Ryan A. Flynn ◽  
Christopher P. Lapointe ◽  
Yaw Shin Ooi ◽  
Michael L. Zhao ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Translational Control ◽  
Ribosomal Proteins ◽  
Cell Types ◽  
Human Cell Line ◽  
Cellular Protein ◽  
Ribosomal Protein Genes ◽  
Genomic Locus ◽  
Cellular Phenotypes

ABSTRACTIn order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Many cell types can nonetheless withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. However, the direct and indirect consequences from sustained alterations in ribosomal protein levels are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation.

scholarly journals Evolution of Ribosomal Protein S14 Demonstrated by the Reconstruction of Chimeric Ribosomes in Bacillus subtilis

2021 ◽  
Vol 203 (10) ◽  
Author(s):  
Genki Akanuma ◽  
Fujio Kawamura ◽  
Satoru Watanabe ◽  
Masaki Watanabe ◽  
Fumiya Okawa ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Binding Motif ◽  
Independent Sequence ◽  
Content Type ◽  
Translational Activity ◽  
Bacterial Ribosome ◽  
70S Ribosome

ABSTRACT Ribosomal protein S14 can be classified into three types. The first, the C+ type has a Zn2+ binding motif and is ancestral. The second and third are the C− short and C− long types, neither of which contain a Zn2+ binding motif and which are ca. 90 residues and 100 residues in length, respectively. In the present study, the C+ type S14 from Bacillus subtilis ribosomes (S14BsC+) were completely replaced by the heterologous C− long type of S14 from Escherichia coli (S14Ec) or Synechococcus elongatus (S14Se). Surprisingly, S14Ec and S14Se were incorporated fully into 70S ribosomes in B. subtilis. However, the growth rates as well as the sporulation efficiency of the mutants harboring heterologous S14 were significantly decreased. In these mutants, the polysome fraction was decreased and the 30S and 50S subunits accumulated unusually, indicating that cellular translational activity of these mutants was decreased. In vitro analysis showed a reduction in the translational activity of the 70S ribosome fraction purified from these mutants. The abundance of ribosomal proteins S2 and S3 in the 30S fraction in these mutants was reduced while that of S14 was not significantly decreased. It seems likely that binding of heterologous S14 changes the structure of the 30S subunit, which causes a decrease in the assembly efficiency of S2 and S3, which are located near the binding site of S14. Moreover, we found that S3 from S. elongatus cannot function in B. subtilis unless S14Se is present. IMPORTANCE S14, an essential ribosomal protein, may have evolved to adapt bacteria to zinc-limited environments by replacement of a zinc-binding motif with a zinc-independent sequence. It was expected that the bacterial ribosome would be tolerant to replacement of S14 because of the previous prediction that the spread of C− type S14 involved horizontal gene transfer. In this study, we completely replaced the C+ type of S14 in B. subtilis ribosome with the heterologous C− long type of S14 and characterized the resulting chimeric ribosomes. Our results suggest that the B. subtilis ribosome is permissive for the replacement of S14, but coevolution of S3 might be required to utilize the C− long type of S14 more effectively.

Regulation of the Escherichia coli S10 ribosomal protein operon by heterologous L4 ribosomal proteins

1995 ◽  
Vol 73 (11-12) ◽  
pp. 1105-1112 ◽  
Author(s):  
Janice M. Zengel ◽  
Dariya Vorozheikina ◽  
Xiao Li ◽  
Lasse Lindahl
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Yersinia Pseudotuberculosis ◽  
Bacillus Stearothermophilus ◽  
Ribosomal Protein Genes ◽  
Haemophilus Influenza ◽  
E Coli ◽  
Autogenous Control ◽  
Ribosomal Protein Operon

We have cloned the L4 ribosomal protein genes from Morganella morganii and Haemophilus influenza. The sequences of these genes were compared with published sequences for Escherichia coli, Yersinia pseudotuberculosis, and Bacillus stearothermophilus. All five of these L4 genes were expressed in E. coli and shown to function as repressors of both transcription and translation of the E. coli S10 operon. Possible implications for regulation of r-protein synthesis in species other than E. coli are discussed.Key words: ribosomes, autogenous control, r-protein L4, phylogeny.

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