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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 22 February 2011, Vol.108(8), pp.3199-203
    Description: Elongation factor 4 (EF4) is one of the most conserved proteins present in bacteria as well as in mitochondria and chloroplasts of eukaryotes. Although EF4 has the unique ability to catalyze the back-translocation reaction on posttranslocation state ribosomes, the physiological role of EF4 remains unclear. Here we demonstrate that EF4 is stored at the membrane of Escherichia coli cells and released into the cytoplasm upon conditions of high ionic strength or low temperature. Under such conditions, wild-type E. coli cells overgrow mutant cells lacking the EF4 gene within 5-10 generations. Elevated intracellular Mg(2+) concentrations or low temperature retard bacterial growth and inhibit protein synthesis, probably because of formation of aberrant elongating ribosomal states. We suggest that EF4 binds to these stuck ribosomes and remobilizes them, consistent with the EF4-dependent enhancement (fivefold) in protein synthesis observed under these unfavorable conditions. The strong selective advantage conferred by the presence of EF4 at high intracellular ionic strength or low temperatures explains the ubiquitous distribution and high conservation of EF4.
    Keywords: Magnesium ; Escherichia Coli Proteins -- Metabolism ; Protein Biosynthesis -- Genetics ; Transcriptional Elongation Factors -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Article
    Article
    Language: English
    In: Journal of bacteriology, November 2014, Vol.196(22), pp.3817-9
    Description: Mg(2+) and K(+) are the prevalent di- and monovalent cations inside the cells in all three domains, playing a dominant role in structure and function of biological macromolecules. Ribosomes bind a substantial fraction of total Mg(2+) and K(+) cations. In this issue of the Journal of Bacteriology, Akanuma and coworkers (G. Akanuma et al., J. Bacteriol. 196:3820-3830, 2014, doi:10.1128/JB.01896-14) report a surprising genetic link between ribosome amounts per cell and the intracellular Mg(2+) concentrations.
    Keywords: Bacillus Subtilis -- Metabolism ; Bacterial Proteins -- Metabolism ; Magnesium -- Metabolism ; Ribosomal Proteins -- Metabolism ; Ribosomes -- Metabolism
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 3
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 30 May 2017, Vol.114(22), pp.E4399-E4407
    Description: Protein biosynthesis is inherently coupled to cotranslational protein folding. Folding of the nascent chain already occurs during synthesis and is mediated by spatial constraints imposed by the ribosomal exit tunnel as well as self-interactions. The polypeptide's vectorial emergence from the ribosomal tunnel establishes the possible folding pathways leading to its native tertiary structure. How cotranslational protein folding and the rate of synthesis are linked to a protein's amino acid sequence is still not well defined. Here, we follow synthesis by individual ribosomes using dual-trap optical tweezers and observe simultaneous folding of the nascent polypeptide chain in real time. We show that observed stalling during translation correlates with slowed peptide bond formation at successive proline sequence positions and electrostatic interactions between positively charged amino acids and the ribosomal tunnel. We also determine possible cotranslational folding sites initiated by hydrophobic collapse for an unstructured and two globular proteins while directly measuring initial cotranslational folding forces. Our study elucidates the intricate relationship among a protein's amino acid sequence, its cotranslational nascent-chain elongation rate, and folding.
    Keywords: Cotranslational Protein Folding ; Optical Tweezers ; Protein Synthesis ; Ribosomes ; Single Molecule ; Protein Biosynthesis ; Protein Folding
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 4
    Language: English
    In: Journal of molecular biology, 04 May 2012, Vol.418(3-4), pp.131-3
    Keywords: Archaeal Proteins -- Chemistry ; Cryoelectron Microscopy -- Methods ; Methanobacteriaceae -- Metabolism ; Prokaryotic Initiation Factors -- Chemistry ; Ribosome Subunits, Large, Archaeal -- Ultrastructure ; Ribosomes -- Genetics
    ISSN: 00222836
    E-ISSN: 1089-8638
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  • 5
    In: Molecular Microbiology, October 2012, Vol.86(1), pp.6-9
    Description: The / system, which is almost universal in bacteria, rescues bacterial ribosomes stalled at the end of non‐stop ( lacking a stop codon). In addition, a few bacteria, including , have developed a second two‐component system as reported by Chadani . (). A small protein, of 55 amino acids (formerly called ), mediates binding of release factor 2 to the ribosomal A site lacking a complete codon and thereby triggers translational termination and rescue of the stalled ribosome.
    Keywords: Escherichia Coli -- Enzymology ; Escherichia Coli Proteins -- Metabolism ; Peptide Termination Factors -- Metabolism ; RNA, Transfer, Amino Acyl -- Metabolism ; RNA-Binding Proteins -- Metabolism ; Ribosomes -- Metabolism;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 01 March 2016, Vol.113(9), pp.E1180-9
    Description: According to the standard model of bacterial translation initiation, the small ribosomal 30S subunit binds to the initiation site of an mRNA with the help of three initiation factors (IF1-IF3). Here, we describe a novel type of initiation termed "70S-scanning initiation," where the 70S ribosome does not necessarily dissociate after translation of a cistron, but rather scans to the initiation site of the downstream cistron. We detailed the mechanism of 70S-scanning initiation by designing unique monocistronic and polycistronic mRNAs harboring translation reporters, and by reconstituting systems to characterize each distinct mode of initiation. Results show that 70S scanning is triggered by fMet-tRNA and does not require energy; the Shine-Dalgarno sequence is an essential recognition element of the initiation site. IF1 and IF3 requirements for the various initiation modes were assessed by the formation of productive initiation complexes leading to synthesis of active proteins. IF3 is essential and IF1 is highly stimulating for the 70S-scanning mode. The task of IF1 appears to be the prevention of untimely interference by ternary aminoacyl (aa)-tRNA•elongation factor thermo unstable (EF-Tu)•GTP complexes. Evidence indicates that at least 50% of bacterial initiation events use the 70S-scanning mode, underscoring the relative importance of this translation initiation mechanism.
    Keywords: 30s-Binding Initiation ; 70s-Scanning Initiation ; Protein Synthesis ; Ribosomal Functions ; Translational Initiation ; Protein Biosynthesis ; Ribosomes -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 7
    Article
    Article
    In: Nature, 1996, Vol.379(6565), p.491
    Description: The elongation factors EF-Tu and EF-G in bacteria and EF-1-alpha and EF-2 in other organisms catalyze the elongation of amino acid chains and regulate protein synthesis. They are similar to G-proteins and switch from inactive to active states by binding GTP and GDP. EF-G catalyzes ribosomal conversion from the pre- to post-translational state, while EF-Tu catalyzes the reverse reaction. The crystal structures of GDP-bound and free EF-G reveal that the tRNA part of the ternary complex, aminoacyl-tRNA.EF-Tu.GTP, and the domains 3 to 5 of EF-G are similar.
    Keywords: G Proteins -- Observations ; Ribosomes -- Research ; Protein Synthesis;
    ISSN: 0028-0836
    E-ISSN: 1476-4687
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  • 8
    In: Nature, 2012, Vol.485(7399), p.526
    Description: Bacterial ribosomes stalled at the 3' end of malfunctioning messenger RNAs can be rescued by transfer-messenger RNA (tmRNA)-mediated trans-translation (1,2). The SmpB protein forms a complex with the tmRNA, and the transfer-RNA-like domain (TLD) of the tmRNA then enters the A site of the ribosome. Subsequently, the TLD-SmpB module is translocated to the P site, a process that is facilitated by the elongation factor EF-G, and translation is switched to the mRNA-like domain (MLD) of the tmRNA. Accurate loading of the MLD into the mRNA path is an unusual initiation mechanism. Despite various snapshots of different ribosome-tmRNA complexes at low to intermediate resolution (3-7), it is unclear how the large, highly structured tmRNA is translocated and how the MLD is loaded. Here we present a cryo-electron microscopy reconstruction of a fusidic-acid-stalled ribosomal 70S-tmRNA-SmpB-EF-G complex (carrying both of the large ligands, that is, EF-G and tmRNA) at 8.3 [Angstrom] resolution. This post-translocational intermediate ([TI.sup.POST]) presents the TLD-SmpB module in an intrasubunit ap/P hybrid site and a [tRNA.sup.fMet] in an intrasubunit pe/E hybrid site. Conformational changes in the ribosome and tmRNA occur in the intersubunit space and on the solvent side. The key underlying event is a unique extra-large swivel movement of the 30S head, which is crucial for both tmRNASmpB translocation and MLD loading, thereby coupling translocation to MLD loading. This mechanism exemplifies the versatile, dynamic nature of the ribosome, and it shows that the conformational modes of the ribosome that normally drive canonical translation can also be used in a modified form to facilitate more complex tasks in specialized non-canonical pathways.
    Keywords: Translocations (Genetics) -- Research ; Ribosomes -- Physiological Aspects ; Messenger Rna -- Physiological Aspects ; Transfer Rna -- Physiological Aspects;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 9
    Language: English
    In: Biophysical Journal, 16 February 2016, Vol.110(3), pp.351a-351a
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.bpj.2015.11.1893 Byline: Alexandros Katranidis, Florian Wruck, Knud H. Nierhaus, Georg Buldt, Martin Hegner Author Affiliation: (1) Forschungszentrum Juelich, ICS-5, Juelich, Germany (2) CRANN-The Naughton Institute, Dublin, Ireland (3) Charite - Universitatsmedizin Berlin, Berlin, Germany (4) Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russian Federation Article Note: (miscellaneous) 1734-Plat
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 10
    Language: English
    In: Journal of Molecular Biology, 11 September 2016, Vol.428(18), pp.3577-3587
    Description: It is general wisdom that termination of bacterial protein synthesis is obligatorily followed by recycling governed by the factors ribosomal recycling factor (RRF), EF-G, and IF3, where the ribosome dissociates into its subunits. In contrast, a recently described 70S-scanning mode of initiation holds that after termination, scanning of 70S can be triggered by fMet-tRNA to the initiation site of a downstream cistron. Here, we analyze the apparent conflict. We constructed a bicistronic mRNA coding for luciferases and showed with a highly resolved system that the expression of the second cistron did not at all depend on the presence of active RRF. An analysis cannot be performed in a straightforward way, since RRF is essential for viability and therefore, the RRF gene cannot be knocked out. However, we found an experimental window, where the RRF amount could be reduced to below 2.5%, and in this situation, the expression of the second cistron of a bicistronic luciferase mRNA was only moderately reduced. Both and results suggested that RRF-dependent recycling is not an obligatory step after termination, in agreement with the previous findings concerning 70S-scanning initiation. In this view, recycling after termination is a special case of the general RRF function, which happens whenever fMet-tRNA is not available for triggering 70S scanning. It is generally accepted that essential RRF is an element of the recycling phase. We present that recycling is not an obligatory phase following termination. The second role of RRF within the functional triad RRF/EF-G•GTP/IF3 seems to be resolving stalled ribosomes regardless whether there is a sense or a stop codon at the ribosomal A site.
    Keywords: Protein Synthesis ; Termination of Protein Synthesis ; Ribosome Recycling ; Rrf Function ; Recycling Phase Not Obligatory ; Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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