scholarly journals Escherichia coli ribosomal protein S1 enhances the kinetics of ribosome biogenesis and RNA decay

2021 ◽  
Author(s):  
Mélodie Duval ◽  
Karine Prévost ◽  
Katarzyna J Bandyra ◽  
Anne-Catherine Helfer ◽  
Alexey Korepanov ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Protein ◽  
Mutant Strain ◽  
Stress Responses ◽  
Ribosome Biogenesis ◽  
Rna Decay ◽  
Rnase E ◽  
Ribosomal Protein S1

Escherichia coli ribosomal protein S1 is essential for translation initiation of mRNAs and for cellular viability. Two oligonucleotide binding (OB)-fold domains located in the C-terminus of S1 are dispensable for growth, but their deletion causes a cold-shock phenotype, loss of motility and deregulation of RNA mediated stress responses. Surprisingly, the expression of the small regulatory RNA RyhB and one of its repressed target mRNA, sodB, are enhanced in the mutant strain lacking the two OB domains. Using in vivo and in vitro approaches, we show that RyhB retains its capacity to repress translation of target mRNAs in the mutant strain but becomes deficient in triggering rapid turnover of those transcripts. In addition, the mutant is defective in of the final step of the RNase E-dependent maturation of the 16S rRNA. This work unveils an unexpected function of S1 in facilitating ribosome biogenesis and RyhB-dependent mRNA decay mediated by the RNA degradosome. Through its RNA chaperone activity, S1 participates to the coupling between ribosome biogenesis, translation, and RNA decay.

scholarly journals Efficacy of trimethoprim in murine experimental infection with a thymidine kinase-deficient mutant of Escherichia coli.

1997 ◽  
Vol 41 (5) ◽  
pp. 1042-1045 ◽  
Author(s):  
T Tokunaga ◽  
K Oka ◽  
A Takemoto ◽  
Y Ohtsubo ◽  
N Gotoh ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Activity ◽  
Thymidine Kinase ◽  
Mutant Strain ◽  
Experimental Infection ◽  
Therapeutic Efficacy ◽  
Parent Strain ◽  
E Coli

The antimicrobial activity of trimethoprim is antagonized by thymidine in in vitro susceptibility tests. The purpose of this investigation was to determine whether this antagonism also occurred during experimental infection in mice, which have high serum thymidine concentrations. We derived a mutant strain of Escherichia coli, TT-48, incapable of utilizing exogenous thymidine from parent strain E. coli KC-14 and then investigated the in vitro and in vivo antimicrobial activities of trimethoprim, sulfamethoxazole, cefdinir, and ofloxacin against these strains. E. coli TT-48 lacked the activity of thymidine kinase, which catalyzes the conversion of thymidine to thymidylate, but its growth curve remained close to that of the parent strain. The MICs of all of the antimicrobial agents tested, except cefdinir, for the mutant strain were slightly inferior to those for the parent strain. The bactericidal effect of trimethoprim against the parent strain was antagonized by thymidine at concentrations of more than 1 microg/ml, while that against the mutant strain was not affected by thymidine even at the highest concentration (10 microg/ml). The therapeutic efficacy of trimethoprim in experimental murine infections was significantly higher when the mutant rather than the parent strain was used, whereas the therapeutic efficacy of cefdinir or ofloxacin, whose antimicrobial action is independent of folic acid synthesis, was the same with both strains. Unexpectedly, sulfamethoxazole also had similar efficacy against both strains. Thus, high thymidine concentrations antagonized the antimicrobial activity of trimethoprim in vitro and in vivo.

scholarly journals Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E

2019 ◽  
Vol 48 (2) ◽  
pp. 847-861 ◽  
Author(s):  
Nida Ali ◽  
Jayaraman Gowrishankar
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Rna Binding ◽  
Initial Step ◽  
Dominant Negative ◽  
Rnase E ◽  
Wild Type ◽  
Catalytic Active Site

Abstract RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5′-sensor pocket that renders enzyme activity maximal on 5′-monophosphorylated RNAs. The protein's non-catalytic C-terminal half (CTH) harbours RNA-binding motifs and serves as scaffold for a multiprotein degradosome complex, but is dispensable for viability. Here, we provide evidence that a full-length hetero-tetramer, composed of a mixture of wild-type and (recessive lethal) active-site mutant subunits, exhibits identical activity in vivo as the wild-type homo-tetramer itself (‘recessive resurrection’). When all of the cognate polypeptides lacked the CTH, the active-site mutant subunits were dominant negative. A pair of C-terminally truncated polypeptides, which were individually inactive because of additional mutations in their active site and 5′-sensor pocket respectively, exhibited catalytic function in combination, both in vivo and in vitro (i.e. intragenic or allelic complementation). Our results indicate that adjacent subunits within an oligomer are separately responsible for 5′-sensing and cleavage, and that RNA binding facilitates oligomerization. We propose also that the CTH mediates a rate-determining initial step for enzyme function, which is likely the binding and channelling of substrate for NTH’s endonucleolytic action.

scholarly journals Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon

Microbiology ◽  
2011 ◽  
Vol 157 (1) ◽  
pp. 66-76 ◽  
Author(s):  
Lena C. Gaubig ◽  
Torsten Waldminghaus ◽  
Franz Narberhaus
Keyword(s):  
Escherichia Coli ◽  
Heat Shock ◽  
Transcriptional Control ◽  
Rnase E ◽  
Translation Control ◽  
E Coli ◽  
Complex Process ◽  
Shock Proteins

The Escherichia coli ibpAB operon encodes two small heat-shock proteins, the inclusion-body-binding proteins IbpA and IbpB. Here, we report that expression of ibpAB is a complex process involving at least four different layers of control, namely transcriptional control, RNA processing, translation control and protein stability. As a typical member of the heat-shock regulon, transcription of the ibpAB operon is controlled by the alternative sigma factor σ 32 (RpoH). Heat-induced transcription of the bicistronic operon is followed by RNase E-mediated processing events, resulting in monocistronic ibpA and ibpB transcripts and short 3′-terminal ibpB fragments. Translation of ibpA is controlled by an RNA thermometer in its 5′ untranslated region, forming a secondary structure that blocks entry of the ribosome at low temperatures. A similar structure upstream of ibpB is functional in vitro but not in vivo, suggesting downregulation of ibpB expression in the presence of IbpA. The recently reported degradation of IbpA and IbpB by the Lon protease and differential regulation of IbpA and IbpB levels in E. coli are discussed.

scholarly journals Ribosomal Protein L12 Uses a Distinct Nuclear Import Pathway Mediated by Importin 11

2002 ◽  
Vol 22 (4) ◽  
pp. 1266-1275 ◽  
Author(s):  
Scott M. Plafker ◽  
Ian G. Macara
Keyword(s):  
Ribosomal Protein ◽  
Nuclear Import ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Protein Import ◽  
Nuclear Translocation ◽  
Nuclear Accumulation ◽  
Transient Transfection Assay

ABSTRACT Ribosome biogenesis requires the nuclear translocation of ribosomal proteins from their site of synthesis in the cytoplasm to the nucleus. Analyses of the import mechanisms have revealed that most ribosomal proteins can be delivered to the nucleus by multiple transport receptors (karyopherins or importins). We now provide evidence that ribosomal protein L12 (rpL12) is distinguished from the bulk of ribosomal proteins because it accesses the importin 11 pathway as a major route into the nucleus. rpL12 specifically and directly interacted with importin 11 in vitro and in vivo. Both rpL12 binding to and import by importin 11 were inhibited by another importin 11 substrate, UbcM2, indicating that these two cargoes may bind overlapping sites on the transport receptor. In contrast, the import of rpL23a, a ribosomal protein that uses the general ribosomal protein import system, was not competed by UbcM2, and in an in vitro binding assay, importin 11 did not bind to the nuclear localization signal of rpL23a. Furthermore, in a transient transfection assay, the nuclear accumulation of rpL12 was increased by coexpressed importin 11, but not by other importins. These data are consistent with importin 11 being a mediator of rpL12 nuclear import. Taken together, these results indicate that rpL12 uses a distinct nuclear import pathway that may contribute to a mechanism for regulating ribosome synthesis and/or maturation.

scholarly journals Sp1-Mediated circRNA circHipk2 Regulates Myogenesis by Targeting Ribosomal Protein Rpl7

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 696
Author(s):  
Junyu Yan ◽  
Yalan Yang ◽  
Xinhao Fan ◽  
Yijie Tang ◽  
Zhonglin Tang
Keyword(s):  
Ribosomal Protein ◽  
Ribosome Biogenesis ◽  
C2c12 Cells ◽  
Circular Rnas ◽  
Exon 2 ◽  
Rna Molecules ◽  
Assembly Factor ◽  
And Function

Circular RNAs (circRNAs) represent a class of covalently closed single-stranded RNA molecules that are emerging as essential regulators of various biological processes. The circRNA circHipk2 originates from exon 2 of the Hipk2 gene in mice and was reported to be involved in acute promyelocytic leukemia and myocardial injury. However, the functions and mechanisms of circHipk2 in myogenesis are largely unknown. Here, to deepen our knowledge about the role of circHipk2, we studied the expression and function of circHipk2 during skeletal myogenesis. We found that circHipk2 was mostly distributed in the cytoplasm, and dynamically and differentially expressed in various myogenesis systems in vitro and in vivo. Functionally, overexpression of circHipk2 inhibited myoblast proliferation and promoted myotube formation in C2C12 cells, whereas the opposite effects were observed after circHipk2 knockdown. Mechanistically, circHipk2 could directly bind to ribosomal protein Rpl7, an essential 60S preribosomal assembly factor, to inhibit ribosome translation. In addition, we verified that transcription factor Sp1 directly bound to the promoter of circHipk2 and affected the expression of Hipk2 and circHipk2 in C2C12 myoblasts. Collectively, these findings identify circHipk2 as a candidate circRNA regulating ribosome biogenesis and myogenesis proliferation and differentiation.

scholarly journals The stoichiometry of E. coli 30S ribosomal protein S1 on in vivo and in vitro polyribosomes

FEBS Letters ◽  
1974 ◽  
Vol 41 (2) ◽  
pp. 323-326 ◽  
Author(s):  
P.H. Van Knippenberg ◽  
P.J.J. Hooykaas ◽  
J. Van Duin
Keyword(s):  
Ribosomal Protein ◽  
E Coli ◽  
Ribosomal Protein S1

scholarly journals Specific Binding of Escherichia coliRibosomal Protein S1 to boxA Transcriptional Antiterminator RNA

1998 ◽  
Vol 180 (8) ◽  
pp. 2248-2252 ◽  
Author(s):  
Jeremy Mogridge ◽  
Jack Greenblatt
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Specific Binding ◽  
Rrna Synthesis ◽  
Bacteriophage Λ ◽  
N Protein ◽  
Ribosomal Protein S1

ABSTRACT We show that ribosomal protein S1 specifically binds theboxA transcriptional antiterminator RNAs of bacteriophage λ and the Escherichia coli ribosomal RNA operons. Although S1 competes with the NusB-S10 antitermination complex for binding to boxA, it does not affect antitermination by the λ N protein in vitro, and its role, if any, in rRNA synthesis is still unknown.

scholarly journals Ribosomal protein S1 influences trans-translation in vitro and in vivo

2007 ◽  
Vol 35 (7) ◽  
pp. 2368-2376 ◽  
Author(s):  
Matthieu Saguy ◽  
Reynald Gillet ◽  
Patricia Skorski ◽  
Sylvie Hermann-Le Denmat ◽  
Brice Felden
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Protein S1
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