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https://www.readbyqxmd.com/read/28538735/ensemble-cryo-em-elucidates-the-mechanism-of-translation-fidelity
#1
Anna B Loveland, Gabriel Demo, Nikolaus Grigorieff, Andrei A Korostelev
Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28368583/thio-modification-of-trna-at-the-wobble-position-as-regulator-of-the-kinetics-of-decoding-and-translocation-on-the-ribosome
#2
Namit Ranjan, Marina V Rodnina
Uridine 34 (U34) at the wobble position of the tRNA anticodon is post-transcriptionally modified, usually to mcm(5)s(2), mcm(5), or mnm(5). The lack of the mcm(5) or s(2) modification at U34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) causes ribosome pausing at the respective codons in yeast. The pauses occur during the elongation step, but the mechanism that triggers ribosome pausing is not known. Here, we show how the s(2) modification in yeast tRNA(Lys) affects mRNA decoding and tRNA-mRNA translocation. Using real-time kinetic analysis we show that mcm(5)-modified tRNA(Lys) lacking the s(2) group has a lower affinity of binding to the cognate codon and is more efficiently rejected than the fully modified tRNA(Lys)...
April 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28362257/role-of-d-aminoacyl-trna-deacylase-beyond-chiral-proofreading-as-a-cellular-defense-against-glycine-mischarging-by-alars
#3
Komal Ishwar Pawar, Katta Suma, Ayshwarya Seenivasan, Santosh Kumar Kuncha, Satya Brata Routh, Shobha P Kruparani, Rajan Sankaranarayanan
Strict L-chiral rejection through Gly-cisPro motif during chiral proofreading underlies the inability of D-aminoacyl-tRNA deacylase (DTD) to discriminate between D-amino acids and achiral glycine. The consequent Gly-tRNA(Gly) 'misediting paradox' is resolved by EF-Tu in the cell. Here, we show that DTD's active site architecture can efficiently edit mischarged Gly-tRNA(Ala) species four orders of magnitude more efficiently than even AlaRS, the only ubiquitous cellular checkpoint known for clearing the error...
March 31, 2017: ELife
https://www.readbyqxmd.com/read/28272393/experimental-vaccine-induces-th1-driven-immune-responses-and-resistance-to-neisseria-gonorrhoeae-infection-in-a-murine-model
#4
Y Liu, L A Hammer, W Liu, M M Hobbs, R A Zielke, A E Sikora, A E Jerse, N K Egilmez, M W Russell
Female mice were immunized intravaginally with gonococcal outer membrane vesicles (OMVs) plus microencapsulated interleukin-12 (IL-12), and challenged using an established model of genital infection with Neisseria gonorrhoeae. Whereas sham-immunized and control animals cleared the infection in 10-13 days, those immunized with OMV plus IL-12 cleared infection with homologous gonococcal strains in 6-9 days. Significant protection was also seen after challenge with antigenically distinct strains of N. gonorrhoeae, and protective anamnestic immunity persisted for at least 6 months after immunization...
March 8, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28255691/the-naringenin-induced-exoproteome-of-rhizobium-etli-ce3
#5
Niurka Meneses, Hermenegildo Taboada, Michael F Dunn, María Del Carmen Vargas, Natasha Buchs, Manfred Heller, Sergio Encarnación
Flavonoids excreted by legume roots induce the expression of symbiotically essential nodulation (nod) genes in rhizobia, as well as that of specific protein export systems. In the bean microsymbiont Rhizobium etli CE3, nod genes are induced by the flavonoid naringenin. In this study, we identified 693 proteins in the exoproteome of strain CE3 grown in minimal medium with or without naringenin, with 101 and 100 exoproteins being exclusive to these conditions, respectively. Four hundred ninety-two (71%) of the extracellular proteins were found in both cultures...
March 2, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28223500/activation-of-contact-dependent-antibacterial-trnase-toxins-by-translation-elongation-factors
#6
Allison M Jones, Fernando Garza-Sánchez, Jaime So, Christopher S Hayes, David A Low
Contact-dependent growth inhibition (CDI) is a mechanism by which bacteria exchange toxins via direct cell-to-cell contact. CDI systems are distributed widely among Gram-negative pathogens and are thought to mediate interstrain competition. Here, we describe tsf mutations that alter the coiled-coil domain of elongation factor Ts (EF-Ts) and confer resistance to the CdiA-CT(EC869) tRNase toxin from enterohemorrhagic Escherichia coli EC869. Although EF-Ts is required for toxicity in vivo, our results indicate that it is dispensable for tRNase activity in vitro...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28202229/requirement-of-the-rna-binding-protein-smpb-during-intracellular-growth-of-listeria-monocytogenes
#7
Mobarak Abu Mraheil, Renate Frantz, Lisa Teubner, Heiko Wendt, Uwe Linne, Jessica Wingerath, Thomas Wirth, Trinad Chakraborty
Bacterial trans-translation is the main quality control mechanism employed to relieve stalled ribosomes. Trans-translation is mediated by the small protein B (SmpB) and transfer-mRNA (tmRNA) ribonucleoprotein complex, which interacts with translational complexes stalled at the 3' end of non-stop mRNAs to release the stalled ribosomes thereby targeting the nascent polypeptides and truncated mRNAs for degradation. The trans-translation system exists with a few exceptions in all bacteria. In the present study, we assessed the contribution of SmpB to the growth and virulence of Listeria monocytogenes, a human intracellular food-borne pathogen that colonizes host tissues to cause severe invasive infections...
April 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28138068/ribosome-dynamics-during-decoding
#8
REVIEW
Marina V Rodnina, Niels Fischer, Cristina Maracci, Holger Stark
Elongation factors Tu (EF-Tu) and SelB are translational GTPases that deliver aminoacyl-tRNAs (aa-tRNAs) to the ribosome. In each canonical round of translation elongation, aa-tRNAs, assisted by EF-Tu, decode mRNA codons and insert the respective amino acid into the growing peptide chain. Stop codons usually lead to translation termination; however, in special cases UGA codons are recoded to selenocysteine (Sec) with the help of SelB. Recruitment of EF-Tu and SelB together with their respective aa-tRNAs to the ribosome is a multistep process...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28132884/novel-mutation-in-mitochondrial-elongation-factor-ef-tu-associated-to-dysplastic-leukoencephalopathy-and-defective-mitochondrial-dna-translation
#9
Michela Di Nottia, Arianna Montanari, Daniela Verrigni, Romina Oliva, Alessandra Torraco, Erika Fernandez-Vizarra, Daria Diodato, Teresa Rizza, Marzia Bianchi, Michela Catteruccia, Massimo Zeviani, Carlo Dionisi-Vici, Silvia Francisci, Enrico Bertini, Rosalba Carrozzo
The mitochondrial Elongation Factor Tu (EF-Tu), encoded by the TUFM gene, is a highly conserved GTPase, which is part of the mitochondrial protein translation machinery. In its activated form it delivers the aminoacyl-tRNAs to the A site of the mitochondrial ribosome. We report here on a baby girl with severe infantile macrocystic leukodystrophy with micropolygyria and a combined defect of complexes I and IV in muscle biopsy, caused by a novel mutation identified in TUFM. Using human mutant cells and the yeast model, we demonstrate the pathological role of the novel variant...
April 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28130490/duplication-of-drosophila-melanogaster-mitochondrial-ef-tu-pre-adaptation-to-t-arm-truncation-and-exclusion-of-bulky-aminoacyl-residues
#10
Aya Sato, Takuma Suematsu, Koh-Ki Aihara, Kiyoshi Kita, Tsutomu Suzuki, Kimitsuna Watanabe, Takashi Ohtsuki, Yoh-Ichi Watanabe
Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aminoacyl-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegans C...
January 27, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28104890/the-receptor-kinase-fer-is-a-ralf-regulated-scaffold-controlling-plant-immune-signaling
#11
Martin Stegmann, Jacqueline Monaghan, Elwira Smakowska-Luzan, Hanna Rovenich, Anita Lehner, Nicholas Holton, Youssef Belkhadir, Cyril Zipfel
In plants, perception of invading pathogens involves cell-surface immune receptor kinases. Here, we report that the Arabidopsis SITE-1 PROTEASE (S1P) cleaves endogenous RAPID ALKALINIZATION FACTOR (RALF) propeptides to inhibit plant immunity. This inhibition is mediated by the malectin-like receptor kinase FERONIA (FER), which otherwise facilitates the ligand-induced complex formation of the immune receptor kinases EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2) with their co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) to initiate immune signaling...
January 20, 2017: Science
https://www.readbyqxmd.com/read/28089773/mitochondrial-diseases-yeast-as-a-model-for-the-study-of-suppressors
#12
Silvia Francisci, Arianna Montanari
Mitochondrial (mt) tRNA gene mutations are an important cause of human morbidity and are associated with different syndromes. We have previously shown that the mitochondrial protein synthesis elongation factor EF-Tu and isolated sequences from the carboxy-terminal domain of yeast and human mt leucyl-tRNA synthetases (LeuRS), have a wide range of suppression capability among different yeast mt tRNA mutants having defective respiratory phenotype. Here we show that the rescuing capability can be restricted to a specific sequence of six amino acids from the carboxy-terminal domain of mt LeuRS...
April 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28043507/t-cell-cytokine-responses-in-peripheral-blood-mononuclear-cells-from-patients-with-multidrug-resistant-tuberculosis-following-stimulation-with-proteins-purified-from-mycobacterium-tuberculosis-mdr-clinical-isolates
#13
Alireza Hadizadeh Tasbiti, Shamsi Yari, Mostafa Ghanei, Seyed Davar Siadat, Amir Amanzadeh, Payam Tabarsi, Keyvan Saeedfar, Ahmadreza Bahrmand
OBJECTIVE: Tuberculosis (TB) is a devastating disease that remains a major health threat worldwide. The appearance of Mycobacterium tuberculosis strains resistance to current antibiotics is a growing problem, both in the third world and in developed countries. Completion of genomic sequencing of M. tuberculosis provides a strong foundation for subsequent identification of proteins to aid the understanding of protein function and the discovery of new drug targets or a TB vaccine. This study employed a proteomics approach to identify proteins from antibiotic resistant M...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27943049/functional-properties-of-lactobacillus-mucosae-strains-isolated-from-brazilian-goat-milk
#14
Georgia Maciel Dias de Moraes, Louricélia Rodrigues de Abreu, Antônio Silvio do Egito, Hévila Oliveira Salles, Liana Maria Ferreira da Silva, Luís Augusto Nero, Svetoslav Dimitrov Todorov, Karina Maria Olbrich Dos Santos
The search for probiotic candidates among lactic acid bacteria (LAB) isolated from food may uncover new strains with promising health and technological properties. Lactobacillus mucosae strains attracted recent research attention due to their ability to adhere to intestinal mucus and to inhibit pathogens in the gastrointestinal tract, both related to a probiotic potential. Properties of interest and safety aspects of three Lb. mucosae strains (CNPC006, CNPC007, and CNPC009) isolated from goat milk were investigated employing in vitro tests...
December 10, 2016: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/27865402/some-proteins-of-m-%C3%A2-tuberculosis-that-localise-to-the-nucleus-of-thp-1-derived-macrophages
#15
Atul Kumar Agrawal, Rajeev Ranjan, Sharat Chandra, Tofan Kumar Rout, Amit Misra, Thota Jagadeshwar Reddy
Host-pathogen dialectics in tuberculosis (TB) via DNA-protein interactions are emerging. We investigated whether proteins produced by Mycobacterium tuberculosis (Mtb) could translocate to the host nucleus. Using lysates of nuclei purified from Mtb-infected THP-1-derived macrophages, we identified at least 15 proteins of Mtb-origin by electrophoretic and chromatographic separation and mass spectrometry. Western blotting confirmed time-dependent accumulation of Mtb EF-Tu, GroEL, GroES and MtrA in the host nucleus...
December 2016: Tuberculosis
https://www.readbyqxmd.com/read/27837019/two-proofreading-steps-amplify-the-accuracy-of-genetic-code-translation
#16
Ka-Weng Ieong, Ülkü Uzun, Maria Selmer, Måns Ehrenberg
Aminoacyl-tRNAs (aa-tRNAs) are selected by the messenger RNA programmed ribosome in ternary complex with elongation factor Tu (EF-Tu) and GTP and then, again, in a proofreading step after GTP hydrolysis on EF-Tu. We use tRNA mutants with different affinities for EF-Tu to demonstrate that proofreading of aa-tRNAs occurs in two consecutive steps. First, aa-tRNAs in ternary complex with EF-Tu·GDP are selected in a step where the accuracy increases linearly with increasing aa-tRNA affinity to EF-Tu. Then, following dissociation of EF-Tu·GDP from the ribosome, the accuracy is further increased in a second and apparently EF-Tu-independent step...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27796304/how-ef-tu-can-contribute-to-efficient-proofreading-of-aa-trna-by-the-ribosome
#17
Jeffrey K Noel, Paul C Whitford
It has long been recognized that the thermodynamics of mRNA-tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical-chemical properties of the ribosome enable proofreading...
October 31, 2016: Nature Communications
https://www.readbyqxmd.com/read/27764940/secretomic-analysis-of-host-pathogen-interactions-reveals-that-elongation-factor-tu-is-a-potential-adherence-factor-of-helicobacter-pylori-during-pathogenesis
#18
Kuo-Hsun Chiu, Ling-Hui Wang, Tsung-Ting Tsai, Huan-Yao Lei, Pao-Chi Liao
The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could, therefore, increase understanding of the mechanisms during initial pathogenesis. The present study used a host-pathogen coculture system of Helicobacter pylori and monocytes (THP-1 cells) to investigate the secreted proteins associated with initial H. pylori pathogenesis. The secreted proteins from the conditioned media from H...
October 20, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27708257/crystal-structures-of-the-human-elongation-factor-eefsec-suggest-a-non-canonical-mechanism-for-selenocysteine-incorporation
#19
Malgorzata Dobosz-Bartoszek, Mark H Pinkerton, Zbyszek Otwinowski, Srinivas Chakravarthy, Dieter Söll, Paul R Copeland, Miljan Simonović
Selenocysteine is the only proteinogenic amino acid encoded by a recoded in-frame UGA codon that does not operate as the canonical opal stop codon. A specialized translation elongation factor, eEFSec in eukaryotes and SelB in prokaryotes, promotes selenocysteine incorporation into selenoproteins by a still poorly understood mechanism. Our structural and biochemical results reveal that four domains of human eEFSec fold into a chalice-like structure that has similar binding affinities for GDP, GTP and other guanine nucleotides...
October 6, 2016: Nature Communications
https://www.readbyqxmd.com/read/27651493/clathrin-dependent-endocytosis-is-required-for-immunity-mediated-by-pattern-recognition-receptor-kinases
#20
Malick Mbengue, Gildas Bourdais, Fabio Gervasi, Martina Beck, Ji Zhou, Thomas Spallek, Sebastian Bartels, Thomas Boller, Takashi Ueda, Hannah Kuhn, Silke Robatzek
Sensing of potential pathogenic bacteria is of critical importance for immunity. In plants, this involves plasma membrane-resident pattern recognition receptors, one of which is the FLAGELLIN SENSING 2 (FLS2) receptor kinase. Ligand-activated FLS2 receptors are internalized into endosomes. However, the extent to which these spatiotemporal dynamics are generally present among pattern recognition receptors (PRRs) and their regulation remain elusive. Using live-cell imaging, we show that at least three other receptor kinases associated with plant immunity, PEP RECEPTOR 1/2 (PEPR1/2) and EF-TU RECEPTOR (EFR), internalize in a ligand-specific manner...
September 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
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