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Replicase
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
It is noteworthy that prior to the identification of replicase subunits III + IV as the EF-TuTs, Travers et al. (1970a,b) had reported that at least one of these subunits was a protein that was called ψr, which stimulated the transcription of ribosomal RNA by the E. coli DNA-dependent RNA polymerase. The involvement of the ψr in the rRNA synthesis has since been challenged (Haseltine 1972). The interest in this question from the RNA phage side was initiated by the fact that the phage-specific RNA synthesis competed in infected cells with the synthesis of ribosomal RNA, as explained in the Phage effect on host section in Chapter 4. However, Travers (1973) subsequently reaffirmed that the EF-Tu did indeed play a critical role in ribosomal RNA synthesis. Then, Travers and Buckland (1973) reported the detection of the RNA polymerase-EF-Tu complexes in vivo. As Kamen (1975) noted, as one of the direct players in this story, the distinct possibility remained that the EF-TuTs complex was normally part of both the transcriptional and translational systems in uninfected bacteria.
Three-Dimensional Structure of p21 and Its Implications
Published in Juan Carlos Lacal, Frank McCormick, The ras Superfamily of GTPases, 2017
EF-Tu is a large GNB protein with 393 amino acids. The three-dimensional structure determination of the Escherichia coli trypsinized EF-Tu has shown that it contains two extra domains in addition to the G domain. These are both mainly comprised of β-sheets.71 The sequence elements corresponding to the effector region of p21, amino acids 45 to 58, were removed by trypsin digestion from EF-Tu to facilitate crystallization.72 This missing region in the structure was indicated by a dashed line as shown in Figure 9A.71 However, on the basis of the structure comparison between p21 and EF-Tu, it seems reasonable to postulate that these amino acids form a loop connecting helix al with β-strand β2 and that this loop is rather located as indicated in Figure 9B. In fact, biochemical cross-linking experiments have proven that this loop must be situated in an analogous position to p21, namely close to the nucleotide.73 Therefore, on the basis of the homology and of these cross-linking experiments, the structure as shown in Figure 9B would be favored.
Guanosine Triphosphate-Binding Proteins
Published in Enrique Pimentel, Handbook of Growth Factors, 2017
Comparison of amino acid sequences has revealed the presence of multiple homologous regions common to all members of the human Ras family and the bacterial translation elongation factors Tu (EF-Tu) and G (EF-G), which also contain in their amino-terminal region a binding site for GTP.114 During protein biosynthesis in bacteria (Escherichia coli), EF-Tu recognizes, transports, and positions the codon-specified aminoacyl-tRNA onto the A site of the ribosome. In this role, EF-Tu interacts with GDP and GTP, which act as allosteric effectors to control the protein conformation required during the elongation cycle.115 High-resolution X-ray diffraction analysis of EF-Tu revealed that four regions of the amino acid sequence that are homologous to human p21ras are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the two proteins interact directly with the GDP ligand.
The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes
Published in Gut Microbes, 2021
Fergus W. J. Collins, Calum J. Walsh, Beatriz Gomez-Sala, Elena Guijarro-García, David Stokes, Klara B. Jakobsdóttir, Kristján Kristjánsson, Finlay Burns, Paul D. Cotter, Mary C. Rea, Colin Hill, R. Paul Ross
Bowtie2 was used to align the paired-end metagenomic reads from the deep-sea dataset against the MEGARes database in order to determine the abundance of known antibiotic resistance genes in the samples.30 Antibiotic resistance genes were found in less than half of all samples analyzed (Table 2). The resistance profile of these samples is dominated by resistance to a class of antibiotics known as elfamycins, which target elongation factor TU (EF-Tu) in bacterial cells.31 Potential resistance to elfamycins was identified in 20 of the metagenomic samples analyzed, in each case due to mutations in the EF-Tu encoding gene tufA. As most bacteria encode two virtually identical copies of the EF-Tu genes, levels of actual resistance due to differences in these genes may be overrepresented.32 As elfamycins are not used therapeutically, the mutations identified here may simply be a result of natural variation in the tufA genes rather than resistance due to the exposure to these antibiotics. EF-Tu has been identified as possibly having an important role in maintaining protein synthesis in response to high-pressure treatment of bacteria, thus potential adaptions of these genes to this environment may confer resistance to these antibiotics.33
Human galectin-1 and galectin-3 promote Tropheryma whipplei infection
Published in Gut Microbes, 2021
Diyoly Ayona, Sandra Madariaga Zarza, Ludovic Landemarre, Benoît Roubinet, Philippe Decloquement, Didier Raoult, Pierre-Edouard Fournier, Benoit Desnues
By using lectin microarray and lectin blotting, we showed that T. whipplei harbors glucose, mannose, fucose, galactose and sialic acid, and expresses several poly-LacNAc-rich glycoproteins which bind both Gal-1 and Gal-3. Some of these glycoproteins were subsequently identified by mass spectrometry. As expected, the identified glycoproteins have previously been reported as membrane-associated in both Gram-positive and Gram-negative bacteria. For example, EF-Tu, which controls several virulence-associated functions, reaches cell surface to interact with host extracellular matrix components such as fibronectin to facilitate adhesion.39 Similarly, the chaperone protein DnaK (Heat-shock protein 70), which plays a critical role in overcoming stress responses is associated with or in close proximity to the membrane.40,41 Interestingly, T. whipplei DnaK seems to play a significant role. Indeed, T. whipplei up-regulates the expression of DnaK upon heat shock42 and patients with classical Whipple’s disease have reduced peripheral T-cell reactivity against DnaK compared to that of healthy controls.43 Finally, and not surprisingly, we also identified WiSP as membrane-associated glycoproteins that bind galectins. Although their role during T. whipplei infection has not been clearly characterized, it was shown that prolonged axenic growth was associated with reduced WiSP glycosylation and impaired intracellular replication in macrophages.16 Overall, our data showed that most of the glycoproteins that we identified bind both Gal-1 and Gal-3, suggesting that galectins may contribute to the pathogenicity of T. whipplei through the interaction with these membrane- and virulence-associated glycoproteins.
Acne vulgaris: new evidence in pathogenesis and future modalities of treatment
Published in Journal of Dermatological Treatment, 2021
NAI: Bacterial elongation factor Tu (EF-Tu) and EF-Ts are interacting proteins involved in polypeptide chain elongation in protein biosynthesis (52). NAI, a semi-synthetic thiopeptide, is a peptide EF-Tu inhibitor, and highly selective against P. acnes, and is currently under evaluation as a 3% gel for acne (2014-001491-62) (36).