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https://www.readbyqxmd.com/read/29155943/logical-engineering-of-d-arm-and-t-stem-of-trna-that-enhances-d-amino-acid-incorporation
#1
Takayuki Katoh, Yoshihiko Iwane, Hiroaki Suga
A bacterial translation factor EF-P alleviates ribosomal stalling caused by polyproline sequence by accelerating Pro-Pro formation. EF-P recognizes a specific D-arm motif found in tRNAPro isoacceptors, 9-nt D-loop closed by a stable D-stem sequence, for Pro-selective peptidyl-transfer acceleration. It is also known that the T-stem sequence on aminoacyl-tRNAs modulates strength of the interaction with EF-Tu, giving enhanced incorporation of non-proteinogenic amino acids such as some N-methyl amino acids. Based on the above knowledge, we logically engineered tRNA's D-arm and T-stem sequences to investigate a series of tRNAs for the improvement of consecutive incorporation of d-amino acids and an α, α-disubstituted amino acid...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29058676/model-based-local-density-sharpening-of-cryo-em-maps
#2
Arjen J Jakobi, Matthias Wilmanns, Carsten Sachse
Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement...
October 23, 2017: ELife
https://www.readbyqxmd.com/read/29045140/the-conformational-change-in-elongation-factor-tu-involves-separation-of-its-domains
#3
Jonathan Lai, Zhaleh Ghaemi, Zaida Luthey-Schulten
Elongation factor Tu (EF-Tu) is a highly conserved GTPase that is responsible for supplying the aminoacylated tRNA to the ribosome. Upon binding to the ribosome, EF-Tu undergoes GTP hydrolysis, which drives a major conformational change, triggering the release of aminoacylated tRNA to the ribosome. Using a combination of molecular simulation techniques, we studied the transition between the pre- and post-hydrolysis structures through two distinct pathways. We show that the transition free energy is minimal along a non-intuitive pathway that involves "separation" of the GTP binding domain (domain 1) from the OB folds (domains 2 and 3), followed by domain 1 rotation, and, eventually, locking the EF-Tu conformation in the post-hydrolysis state...
October 27, 2017: Biochemistry
https://www.readbyqxmd.com/read/29033958/enhanced-bacterial-wilt-resistance-in-potato-through-expression-of-arabidopsis-efr-and-introgression-of-quantitative-resistance-from-solanum-commersonii
#4
Federico Boschi, Claudia Schvartzman, Sara Murchio, Virginia Ferreira, Maria I Siri, Guillermo A Galván, Matthew Smoker, Lena Stransfeld, Cyril Zipfel, Francisco L Vilaró, Marco Dalla-Rizza
Bacterial wilt (BW) caused by Ralstonia solanacearum is responsible for substantial losses in cultivated potato (Solanum tuberosum) crops worldwide. Resistance genes have been identified in wild species; however, introduction of these through classical breeding has achieved only partial resistance, which has been linked to poor agronomic performance. The Arabidopsis thaliana (At) pattern recognition receptor elongation factor-Tu (EF-Tu) receptor (EFR) recognizes the bacterial pathogen-associated molecular pattern EF-Tu (and its derived peptide elf18) to confer anti-bacterial immunity...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28973472/structure-of-a-novel-antibacterial-toxin-that-exploits-elongation-factor-tu-to-cleave-specific-transfer-rnas
#5
Karolina Michalska, Grant C Gucinski, Fernando Garza-Sánchez, Parker M Johnson, Lucy M Stols, William H Eschenfeldt, Gyorgy Babnigg, David A Low, Celia W Goulding, Andrzej Joachimiak, Christopher S Hayes
Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28910101/anisotropic-fluctuations-in-the-ribosome-determine-trna-kinetics
#6
Huan Yang, Jeffrey K Noel, Paul C Whitford
The ribosome is a large ribonucleoprotein complex that is responsible for the production of proteins in all organisms. Accommodation is the process by which an incoming aminoacyl-tRNA (aa-tRNA) molecule binds the ribosomal A site, and its kinetics has been implicated in the accuracy of tRNA selection. In addition to rearrangements in the aa-tRNA molecule, the L11 stalk can undergo large-scale anisotropic motions during translation. To explore the potential impact of this protruding region on the rate of aa-tRNA accommodation, we used molecular dynamics simulations with a simplified model to evaluate the free energy as a function of aa-tRNA position...
October 2, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28894125/elongation-factor-tu-is-a-multifunctional-and-processed-moonlighting-protein
#7
Michael Widjaja, Kate Louise Harvey, Lisa Hagemann, Iain James Berry, Veronica Maria Jarocki, Benjamin Bernard Armando Raymond, Jessica Leigh Tacchi, Anne Gründel, Joel Ricky Steele, Matthew Paul Padula, Ian George Charles, Roger Dumke, Steven Philip Djordjevic
Many bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (SaEf-Tu) and Mycoplasma pneumoniae (MpnEf-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (MhpEf-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28866886/efficient-expression-of-glutathione-peroxidase-with-chimeric-trna-in-amber-less-escherichia-coli
#8
Zhenlin Fan, Jian Song, Tuchen Guan, Xiuxiu Lv, Jingyan Wei
The active center of selenium-containing glutathione peroxidase (GPx) is selenocysteine (Sec), which is is biosynthesized on its tRNA in organisms. The decoding of Sec depends on a specific elongation factor and a Sec Insertion Sequence (SECIS) to suppress the UGA codon. The expression of mammalian GPx is extremely difficult with traditional recombinant DNA technology. Recently, a chimeric tRNA (tRNA(UTu)) that is compatible with elongation factor Tu (EF-Tu) has made selenoprotein expression easier. In this study, human glutathione peroxidase (hGPx) was expressed in amber-less Escherichia coli C321...
September 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28865219/expression-and-immunological-evaluation-of-elongation-factor-tu-of-streptococcus-suis-serotype-2
#9
X J Xia, L Wang, L K Cheng, Z Q Shen, S G Li, J L Wang
Streptococcus suis serotype 2 (SS2) is considered as a major pathogen that causes sepsis and meningitis in piglets and humans, but knowledge of its antigenic proteins remains limited so far. The surface-related proteins of pathogens often play significant roles in bacterium-host interactions and infection. Here, we obtained the elongation factor Tu (EF-Tu) gene of Streptococcus suis and constructed the recombinant expression plasmid successfully. The target recombinant plasmid was then expressed in Escherichia coli and the immuno-protection of the recombinant protein was subsequently evaluated as well...
March 1, 2017: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28865072/gallibacterium-elongation-factor-tu-possesses-amyloid-like-protein-characteristics-participates-in-cell-adhesion-and-is-present-in-biofilms
#10
Jaqueline López-Ochoa, J Fernando Montes-García, Candelario Vázquez, Patricia Sánchez-Alonso, Victor M Pérez-Márquez, Patrick J Blackall, Sergio Vaca, Erasmo Negrete-Abascal
Gallibacterium, which is a bacterial pathogen in chickens, can form biofilms. Amyloid proteins present in biofilms bind Congo red dye. The aim of this study was to characterize the cell-surface amyloid-like protein expressed in biofilms formed by Gallibacterium strains and determine the relationship between this protein and curli, which is an amyloid protein that is commonly expressed by members of the Enterobacteriaceae family. The presence of amyloid-like proteins in outer membrane protein samples from three strains of G...
September 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28851849/functional-constraints-on-replacing-an-essential-gene-with-its-ancient-and-modern-homologs
#11
Betül Kacar, Eva Garmendia, Nurcan Tuncbag, Dan I Andersson, Diarmaid Hughes
Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms...
August 29, 2017: MBio
https://www.readbyqxmd.com/read/28771131/comparative-proteomic-profiles-reveal-characteristic-mycobacterium-tuberculosis-proteins-induced-by-cholesterol-during-dormancy-conditions
#12
Lazaro Garcia-Morales, Lizbel Leon-Solis, Irma E Monroy-Muñoz, Moises Talavera-Paulin, Jeanet Serafin-López, Iris Estrada-Garcia, Sandra Rivera-Gutierrez, Jorge F Cerna-Cortes, Addy C Helguera-Repetto, Jorge A Gonzalez-Y-Merchand
Cholesterol has been reported to play an important role during Mycobacterium tuberculosis infection and during its dormant state inside the host. We present the determination of proteomic profiles of M. tuberculosis H37Rv in the presence of cholesterol as the sole carbon source under exponential growth and in two in vitro dormancy phases (NRP1 and NRP2). Using 2D-PAGE, we detected that M. tuberculosis expressed a high diversity of proteins in both exponential and non-replicative phases. We also found that cholesterol was involved in the overexpression of some proteins related to sulfur metabolism (CysA2), electron transport (FixB), cell wall synthesis (Ald), iron storage (BfrB), protein synthesis (Tig and EF-Tu) and dormancy maintenance (HspX and TB 31...
August 4, 2017: Microbiology
https://www.readbyqxmd.com/read/28751745/translational-roles-of-the-c75-2-oh-in-an-in-vitro-trna-transcript-at-the-ribosomal-a-p-and-e-sites
#13
Jinfan Wang, Anthony C Forster
Aminoacyl-tRNAs containing a deoxy substitution in the penultimate nucleotide (C75 2'OH → 2'H) have been widely used in translation for incorporation of unnatural amino acids (AAs). However, this supposedly innocuous modification surprisingly increased peptidyl-tRNA(Ala)ugc drop off in biochemical assays of successive incorporations. Here we predict the function of this tRNA 2'OH in the ribosomal A, P and E sites using recent co-crystal structures of ribosomes and tRNA substrates and test these structure-function models by systematic kinetics analyses...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28736082/differential-proteome-expression-analysis-of-androgen-dependent-and-independent-pathways-in-lncap-prostate-cancer-cells
#14
Seho Cha, Dong Hoon Shin, Jun Ryeong Seok, Jae Kyung Myung
Prostate cancer (PC) is one of the leading causes of cancer death in men. It commonly develops in older males, but the number of younger men diagnosed with the disease has increased in recent years. Hormone therapies, such as chemical and surgical methods that inhibit androgen synthesis or androgen receptor (AR) activation, have been used for advanced disease. However, castration-resistant PC (CRPC), which exhibits androgen-independent mechanisms for activating AR, develops after a few years of such treatment and no therapy is available...
October 1, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28710887/elfamycins-inhibitors-of-elongation-factor-tu
#15
REVIEW
Samantha M Prezioso, Nicole E Brown, Joanna B Goldberg
Elfamycins are a relatively understudied group of antibiotics that target the essential process of translation through impairment of EF-Tu function. For the most part, the utility of these compounds has been as laboratory tools for the study of EF-Tu and the ribosome, as their poor pharmacokinetic profile and solubility has prevented implementation as therapeutic agents. However, due to the slowing of the antibiotic pipeline and the rapid emergence of resistance to approved antibiotics, this group is being reconsidered...
July 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28699103/expansion-of-pathogen-recognition-specificity-in-plants-using-pattern-recognition-receptors-and-artificially-designed-decoys
#16
REVIEW
Lifan Sun, Jun Qin, Kailun Wang, Jie Zhang
Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) are recognized by plant pattern recognition receptors (PRRs) localized on the cell surface to activate immune responses. This PAMP-triggered immunity (PTI) confers resistance to a broad range of pathogenic microbes and, therefore, has a great potential for genetically engineering broad-spectrum resistance by transferring PRRs across plant families. Pathogenic effectors secreted by phytopathogens often directly target and inhibit key components of PTI signaling pathways via diverse biochemical mechanisms...
July 10, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28645610/inhibition-of-mitochondrial-translation-effectively-sensitizes-renal-cell-carcinoma-to-chemotherapy
#17
Bo Wang, Jinsong Ao, Dan Yu, Ting Rao, Yuan Ruan, Xiaobin Yao
The functional importance of mitochondrial protein translation has been recently documented in the context of various cancers but not renal cell carcinoma (RCC). In lines with these efforts, our work demonstrates that mitochondrial translation inhibition by tigecycline or depletion of EF-Tu mitochondrial translation factor effectively targets RCC and significantly sensitizes RCC response to chemotherapy. We show that antibiotic tigecycline inhibits multiple biological functions of RCC, including growth, colony formation and survival...
August 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28592876/elongation-factor-tu-on-escherichia-coli-isolated-from-urine-of-kidney-stone-patients-promotes-calcium-oxalate-crystal-growth-and-aggregation
#18
Piyawan Amimanan, Ratree Tavichakorntrakool, Kedsarin Fong-Ngern, Pipat Sribenjalux, Aroonlug Lulitanond, Vitoon Prasongwatana, Chaisiri Wongkham, Patcharee Boonsiri, Jariya Umka Welbat, Visith Thongboonkerd
Escherichia coli is the most common bacterium isolated from urine and stone matrix of calcium oxalate (CaOx) stone formers. Whether it has pathogenic role(s) in kidney stone formation or is only entrapped inside the stone remains unclear. We thus evaluated differences between E. coli isolated from urine of patients with kidney stone (EUK) and that from patients with urinary tract infection (UTI) without stone (EUU). From 100 stone formers and 200 UTI patients, only four pairs of EUK/EUU isolates had identical antimicrobial susceptibility patterns...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28589129/whole-genome-sequence-analysis-of-antimicrobial-resistance-genes-in-streptococcus-uberis-and-streptococcus-dysgalactiae-isolates-from-canadian-dairy-herds
#19
Julián Reyes Vélez, Marguerite Cameron, Juan Carlos Rodríguez-Lecompte, Fangfang Xia, Luke C Heider, Matthew Saab, J Trenton McClure, Javier Sánchez
The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine-cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28588135/spatial-distribution-and-ribosome-binding-dynamics-of-ef-p-in-live-escherichia%C3%A2-coli
#20
Sonisilpa Mohapatra, Heejun Choi, Xueliang Ge, Suparna Sanyal, James C Weisshaar
In vitro assays find that ribosomes form peptide bonds to proline (Pro) residues more slowly than to other residues. Ribosome profiling shows that stalling at Pro-Pro-X triplets is especially severe but is largely alleviated in Escherichia coli by the action of elongation factor EF-P. EF-P and its eukaryotic/archaeal homolog IF5A enhance the peptidyl transfer step of elongation. Here, a superresolution fluorescence localization and tracking study of EF-P-mEos2 in live E. coli provides the first in vivo information about the spatial distribution and on-off binding kinetics of EF-P...
June 6, 2017: MBio
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