scholarly journals 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5620 ◽  
Author(s):  
Sergey Levitskii ◽  
Ksenia Derbikova ◽  
Maria V. Baleva ◽  
Anton Kuzmenko ◽  
Andrey V. Golovin ◽  
...  
Keyword(s):  
Dynamic Equilibrium ◽  
Translation Termination ◽  
Protein Biosynthesis ◽  
Sedimentation Coefficient ◽  
Initiation Factor ◽  
Dynamic State ◽  
Bacterial Cells ◽  
E Coli ◽  
Bacterial Ribosome

The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome.

scholarly journals An intermediate state of bacterial ribosome dissociation is fixed by yeast mitochondrial initiation factor 3

2018 ◽  
Author(s):  
Sergey Levitskii ◽  
Ksenia Derbikova ◽  
Andrey V Golovin ◽  
Anton Kuzmenko ◽  
Maria V Baleva ◽  
...  
Keyword(s):  
Intermediate State ◽  
Translation Termination ◽  
Protein Biosynthesis ◽  
Sedimentation Coefficient ◽  
Initiation Factor ◽  
Bacterial Cells ◽  
Ribosomal Subunits ◽  
Bacterial Ribosome ◽  
Dissociated State

The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with the large subunits. In this work, we have exchanged IF3 in E.coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E.coli ribosomes into subunits. Instead, it fixes an intermediate state of ribosomes dissociation characterized by sedimentation coefficient about 60S. Using molecular modeling, we show that such fixation is due to mitochondria-specific terminal extensions of Aim23p that stabilize the position of the protein on the bacterial ribosome.

scholarly journals An intermediate state of bacterial ribosome dissociation is fixed by yeast mitochondrial initiation factor 3

2018 ◽  
Author(s):  
Sergey Levitskii ◽  
Ksenia Derbikova ◽  
Andrey V Golovin ◽  
Anton Kuzmenko ◽  
Maria V Baleva ◽  
...  
Keyword(s):  
Intermediate State ◽  
Translation Termination ◽  
Protein Biosynthesis ◽  
Sedimentation Coefficient ◽  
Initiation Factor ◽  
Bacterial Cells ◽  
Ribosomal Subunits ◽  
Bacterial Ribosome ◽  
Dissociated State

The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with the large subunits. In this work, we have exchanged IF3 in E.coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E.coli ribosomes into subunits. Instead, it fixes an intermediate state of ribosomes dissociation characterized by sedimentation coefficient about 60S. Using molecular modeling, we show that such fixation is due to mitochondria-specific terminal extensions of Aim23p that stabilize the position of the protein on the bacterial ribosome.

scholarly journals CTELS: A Cell-Free System for the Analysis of Translation Termination Rate

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 911 ◽  
Author(s):  
Kseniya A. Lashkevich ◽  
Valeriya I. Shlyk ◽  
Artem S. Kushchenko ◽  
Vadim N. Gladyshev ◽  
Elena Z. Alkalaeva ◽  
...  
Keyword(s):  
Stop Codon ◽  
Translation Termination ◽  
Protein Biosynthesis ◽  
Inhibitory Effect ◽  
In Vitro Translation ◽  
Nonsense Suppression ◽  
Translation System ◽  
Free System ◽  
Termination Rate

Translation termination is the final step in protein biosynthesis when the synthesized polypeptide is released from the ribosome. Understanding this complex process is important for treatment of many human disorders caused by nonsense mutations in important genes. Here, we present a new method for the analysis of translation termination rate in cell-free systems, CTELS (for C-terminally extended luciferase-based system). This approach was based on a continuously measured luciferase activity during in vitro translation reaction of two reporter mRNA, one of which encodes a C-terminally extended luciferase. This extension occupies a ribosomal polypeptide tunnel and lets the completely synthesized enzyme be active before translation termination occurs, i.e., when it is still on the ribosome. In contrast, luciferase molecule without the extension emits light only after its release. Comparing the translation dynamics of these two reporters allows visualization of a delay corresponding to the translation termination event. We demonstrated applicability of this approach for investigating the effects of cis- and trans-acting components, including small molecule inhibitors and read-through inducing sequences, on the translation termination rate. With CTELS, we systematically assessed negative effects of decreased 3′ UTR length, specifically on termination. We also showed that blasticidin S implements its inhibitory effect on eukaryotic translation system, mostly by affecting elongation, and that an excess of eRF1 termination factor (both the wild-type and a non-catalytic AGQ mutant) can interfere with elongation. Analysis of read-through mechanics with CTELS revealed a transient stalling event at a “leaky” stop codon context, which likely defines the basis of nonsense suppression.

scholarly journals Microencapsulation of Enteric Bacteriophages in a pH-Responsive Solid Oral Dosage Formulation Using a Scalable Membrane Emulsification Process

Pharmaceutics ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 475 ◽  
Author(s):  
Vinner ◽  
Richards ◽  
Leppanen ◽  
Sagona ◽  
Malik
Keyword(s):  
Epithelial Cells ◽  
Prolonged Exposure ◽  
Oral Dosage ◽  
Bacterial Cells ◽  
Ph Responsive ◽  
Ion Milling ◽  
Membrane Emulsification ◽  
E Coli ◽  
Emulsification Process

A scalable low-shear membrane emulsification process was used to produce microencapsulated Escherichia coli-phages in a solid oral dosage form. Uniform pH-responsive composite microparticles (mean size ~100 µm) composed of Eudragit® S100 and alginate were produced. The internal microstructure of the gelled microcapsules was studied using ion-milling and imaging, which showed that the microparticles had a solid internal core. The microencapsulation process significantly protected phages upon prolonged exposure to a simulated gastric acidic environment. Encapsulated phages that had been pre-exposed to simulated gastric acid were added to actively growing bacterial cells using in vitro cell cultures and were found to be effective in killing E. coli. Encapsulated phages were also shown to be effective in killing actively growing E. coli in the presence of human epithelial cells. Confocal microscopy images showed that the morphology of encapsulated phage-treated epithelial cells was considerably better than controls without phage treatment. The encapsulated phages were stable during refrigerated storage over a four-week period. The process of membrane emulsification is highly scalable and is a promising route to produce industrial quantities of pH-responsive oral solid dosage forms suitable for delivering high titres of viable phages to the gastrointestinal tract.

scholarly journals Np4A alarmones function in bacteria as precursors to RNA caps

2020 ◽  
Vol 117 (7) ◽  
pp. 3560-3567 ◽  
Author(s):  
Daniel J. Luciano ◽  
Joel G. Belasco
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Promoter Sequence ◽  
Rna Degradation ◽  
Initiation Site ◽  
Bacterial Cells ◽  
E Coli ◽  
N Incorporation ◽  
Nascent Transcripts

Stresses that increase the cellular concentration of dinucleoside tetraphosphates (Np4Ns) have recently been shown to impact RNA degradation by inducing nucleoside tetraphosphate (Np4) capping of bacterial transcripts. However, neither the mechanism by which such caps are acquired nor the function of Np4Ns in bacteria is known. Here we report that promoter sequence changes upstream of the site of transcription initiation similarly affect both the efficiency with which Escherichia coli RNA polymerase incorporates dinucleoside polyphosphates at the 5′ end of nascent transcripts in vitro and the percentage of transcripts that are Np4-capped in E. coli, clear evidence for Np4 cap acquisition by Np4N incorporation during transcription initiation in bacterial cells. E. coli RNA polymerase initiates transcription more efficiently with Np4As than with ATP, particularly when the coding strand nucleotide that immediately precedes the initiation site is a purine. Together, these findings indicate that Np4Ns function in bacteria as precursors to Np4 caps and that RNA polymerase has evolved a predilection for synthesizing capped RNA whenever such precursors are abundant.

scholarly journals Inactivation of the Elongation Factor Tu by Mosquitocidal Toxin-Catalyzed Mono-ADP-Ribosylation

2002 ◽  
Vol 68 (10) ◽  
pp. 4894-4899 ◽  
Author(s):  
Jörg Schirmer ◽  
Hans-Joachim Wieden ◽  
Marina V. Rodnina ◽  
Klaus Aktories
Keyword(s):  
Peptide Mapping ◽  
Elongation Factor ◽  
Bacillus Sphaericus ◽  
Elongation Factor Tu ◽  
Bacterial Cells ◽  
Single Chain ◽  
E Coli ◽  
Adp Ribosylation ◽  
Flight Mass Spectrometry

ABSTRACT The mosquitocidal toxin (MTX) produced by Bacillus sphaericus strain SSII-1 is an ∼97-kDa single-chain toxin which contains a 27-kDa enzyme domain harboring ADP-ribosyltransferase activity and a 70-kDa putative binding domain. Due to cytotoxicity toward bacterial cells, the 27-kDa enzyme fragment cannot be produced in Escherichia coli expression systems. However, a nontoxic 32-kDa N-terminal truncation of MTX can be expressed in E. coli and subsequently cleaved to an active 27-kDa enzyme fragment. In vitro the 27-kDa enzyme fragment of MTX ADP-ribosylated numerous proteins in E. coli lysates, with dominant labeling of an ∼45-kDa protein. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry combined with peptide mapping identified this protein as the E. coli elongation factor Tu (EF-Tu). ADP ribosylation of purified EF-Tu prevented the formation of the stable ternary EF-Tuaminoacyl-tRNAGTP complex, whereas the binding of GTP to EF-Tu was not altered. The inactivation of EF-Tu by MTX-mediated ADP-ribosylation and the resulting inhibition of bacterial protein synthesis are likely to play important roles in the cytotoxicity of the 27-kDa enzyme fragment of MTX toward E. coli.

scholarly journals Participation of X47-fluorescamine modified E. coli tRNAs in in vitro protein biosynthesis

1978 ◽  
Vol 5 (12) ◽  
pp. 4837-4854 ◽  
Author(s):  
Mathias Sprinzl ◽  
Heinz G. Faulhammer
Keyword(s):  
Protein Biosynthesis ◽  
E Coli ◽  
Vitro Protein

scholarly journals Conserved mechanism of cell-wall synthase regulation revealed by the identification of a new PBP activator inPseudomonas aeruginosa

2018 ◽  
Vol 115 (12) ◽  
pp. 3150-3155 ◽  
Author(s):  
Neil G. Greene ◽  
Coralie Fumeaux ◽  
Thomas G. Bernhardt
Keyword(s):  
Cell Wall ◽  
Drug Targets ◽  
Bacterial Cells ◽  
Acinetobacter Baylyi ◽  
Gram Negative ◽  
E Coli ◽  
Outer Membrane Lipoprotein ◽  
Synthase Regulation

Penicillin-binding proteins (PBPs) are synthases required to build the essential peptidoglycan (PG) cell wall surrounding most bacterial cells. The mechanisms regulating the activity of these enzymes to control PG synthesis remain surprisingly poorly defined given their status as key antibiotic targets. Several years ago, the outer-membrane lipoproteinEcLpoB was identified as a critical activator ofEscherichia coliPBP1b (EcPBP1b), one of the major PG synthases of this organism. Activation ofEcPBP1b is mediated through the association ofEcLpoB with a regulatory domain onEcPBP1b called UB2H. Notably,Pseudomonas aeruginosaalso encodes PBP1b (PaPBP1b), which possesses a UB2H domain, but this bacterium lacks an identifiable LpoB homolog. We therefore searched for potentialPaPBP1b activators and identified a lipoprotein unrelated to LpoB that is required for the in vivo activity ofPaPBP1b. We named this protein LpoP and found that it interacts directly withPaPBP1b in vitro and is conserved in many Gram-negative species. Importantly, we also demonstrated thatPaLpoP-PaPBP1b as well as an equivalent protein pair fromAcinetobacter baylyican fully substitute forEcLpoB-EcPBP1b inE. colifor PG synthesis. Furthermore, we show that amino acid changes inPaPBP1b that bypass thePaLpoP requirement map to similar locations in the protein as changes promotingEcLpoB bypass inEcPBP1b. Overall, our results indicate that, although different Gram-negative bacteria activate their PBP1b synthases with distinct lipoproteins, they stimulate the activity of these important drug targets using a conserved mechanism.

scholarly journals Lack of inhibition by l-1-chloro-4-phenyl-3-toluene-p-sulphoamidobutan-2-one (l-1-tosylamido-2-phenylethyl chloromethyl ketone) of the formation of bacterial polypeptide chain initiation complex (Short Communication)

1973 ◽  
Vol 136 (2) ◽  
pp. 433-436 ◽  
Author(s):  
J. Jonák ◽  
B. F. C. Clark
Keyword(s):  
Short Communication ◽  
Polypeptide Chain ◽  
Protein Biosynthesis ◽  
Elongation Factor ◽  
Initiation Factor ◽  
Chain Elongation ◽  
Initiation Complex ◽  
Chloromethyl Ketone ◽  
Chain Initiation

The chymotrypsin inhibitor l-1-chloro-4-phenyl-3-toluene-p-sulphonamidobutan-2-one does not inhibit the function of the initiation factor during the formation of the polypeptide chain initiation complex in vitro. Since the inhibitor has been shown previously to inhibit polypeptide chain elongation by reacting with elongation factor EF-Tu, the inhibitor can be used to investigate the initiation and elongation steps of protein biosynthesis separately.

Synthese, in vivo- und in vitro-Untersuchungen zur tumorhemmenden Wirkung von cis-Dichloro-dipeptidester-platin(II)-Komplexen / Synthesis, in vivo and in vitro Studies on the Antineoplastic Effect of cis-Dichloro-dipeptide Ester Platinum(II) Complexes

1976 ◽  
Vol 31 (6) ◽  
pp. 832-845 ◽  
Author(s):  
Wolfgang Beck ◽  
Bernhard Purucker ◽  
Michael Girnth ◽  
Helmut Schönenberger ◽  
Horst Seidenberger ◽  
...  
Keyword(s):  
Protein Biosynthesis ◽  
Sarcoma 180 ◽  
Protecting Group ◽  
Yoshida Sarcoma ◽  
Walker 256 Carcinosarcoma ◽  
E Coli ◽  
Antineoplastic Effect ◽  
Walker 256

cis-Dichlorodipeptide esterplatinum complexesCl2Pt(MetGlyOEt),Cl2Pt(EthionylGlyOEt), Cl2Pt(GlyGlyOEt)2 and Cl2Pt(GlySerOEt)2 are prepared from the α-amino acid complexes by peptide synthesis using platinum as an amino protecting group. cis-Cl2Pt(GlyGlyOEt)2 and cis-Cl2Pt(GlySerOEt)2 have been prepared also directly from K2PtCl4 and the dipeptidesters. cis-Cl2Pt(GlyGlyOEt)2 (2 a) and cis-Cl2Pt(NH3)2 (5) lead to a prefered inhibition of the DNA-synthesis of sarcoma 180, Yoshida-sarcoma and Walker-256-carcinosarcoma in vitro; RNA- and protein biosynthesis are influenced to a much lower degree. 2a and 5 cause filamentous growth in Escherichia coli B. The DNA polymerase deficient strain of E. coli, p 3478 pol A-, is more inhibited by 2 a and 5 than the non deficient strain W 3110 pol A+. Tumor growth of di-2-chloro-ethylmethylamine (HN2) resistant sarcoma 180 and of Yoshida sarcoma is weakly inhibited, whereas Walker-256-carcinosarcoma is markedly inhibited; however 2a and 5 show similar inhibition of the same tumor.

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