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https://www.readbyqxmd.com/read/29660239/the-population-genetic-test-tajima-s-d-identifies-genes-encoding-pathogen-associated-molecular-patterns-and-other-virulence-related-genes-in-ralstonia-solanacearum
#1
Noam Eckshtain-Levi, Alexandra J Weisberg, Boris A Vinatzer
Detection of pathogen-associated molecular patterns (PAMPs) by plant pattern receptors (PRRs) is an essential part of plant immunity. Until recently, elf18, an epitope of elongation factor tu (EF-Tu), was the sole confirmed PAMP of Ralstonia solanacearum, the causal agent of bacterial wilt disease, limiting our understanding of R. solanacearum - plant interactions. Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs...
April 16, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29649442/the-receptor-like-cytoplasmic-kinase-bik1-localizes-to-the-nucleus-and-regulates-defense-hormone-expression-during-plant-innate-immunity
#2
Neeraj K Lal, Ugrappa Nagalakshmi, Nicholas K Hurlburt, Rosalva Flores, Aurelie Bak, Pyae Sone, Xiyu Ma, Gaoyuan Song, Justin Walley, Libo Shan, Ping He, Clare Casteel, Andrew J Fisher, Savithramma P Dinesh-Kumar
Plants employ cell-surface pattern recognition receptors (PRRs) to detect pathogens. Although phytohormones produced during PRR signaling play an essential role in innate immunity, a direct link between PRR activation and hormone regulation is unknown. EFR is a PRR that recognizes bacterial EF-Tu and activates immune signaling. Here we report that EFR regulates the phytohormone jasmonic acid (JA) through direct phosphorylation of a receptor-like cytoplasmic kinase, BIK1. The BIK1 structure revealed that the EFR-phosphorylated sites reside on a uniquely extended loop away from the BIK1 kinase core domain...
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29627237/immunogenicity-and-protective-capacity-of-ef-tu-and-ftsz-of-streptococcus-suis-serotype-2-against-lethal-infection
#3
Liping Feng, Xiaona Niu, Wen Mei, Weitian Li, Yuan Liu, Stephan P Willias, Chao Yuan, Weicheng Bei, Xiaohong Wang, Jinquan Li
Vaccine development efforts against Streptococcus suis serotype 2 (S. suis 2) are often constrained by strain/serotype antigen variability. Bioinformatics analyses revealed two highly conserved S. suis 2 factors, EF-Tu and FtsZ. Murine immunization with recombinant proteins emulsified in white oil adjuvant or eukaryotic DNA vaccine vectors provided significant protection against lethal S. suis 2 challenge. Immune responses elicited by recombinant protein immunization revealed the robust generation of humoral immune responses, with a mixed induction of Th1-type and Th2-type responses...
April 4, 2018: Vaccine
https://www.readbyqxmd.com/read/29603442/co-evolution-with-recombination-affects-the-stability-of-mobile-genetic-element-insertions-within-gene-families-of-salmonella
#4
Gerrit Brandis, Sha Cao, Diarmaid Hughes
Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF-Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood...
March 30, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29555379/on-elongation-factor-eefsec-its-role-and-mechanism-during-selenium-incorporation-into-nascent-selenoproteins
#5
REVIEW
Miljan Simonović, Anupama K Puppala
BACKGROUND: Selenium, an essential dietary micronutrient, is incorporated into proteins as the amino acid selenocysteine (Sec) in response to in-frame UGA codons. Complex machinery ensures accurate recoding of Sec codons in higher organisms. A specialized elongation factor eEFSec is central to the process. SCOPE OF REVIEW: Selenoprotein synthesis relies on selenocysteinyl-tRNASec (Sec-tRNASec ), selenocysteine inserting sequence (SECIS) and other selenoprotein mRNA elements, an in-trans SECIS binding protein 2 (SBP2) protein factor, and eEFSec...
March 16, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29546243/phosphorylation-decelerates-conformational-dynamics-in-bacterial-translation-elongation-factors
#6
Ariel Talavera, Jelle Hendrix, Wim Versées, Dukas Jurėnas, Katleen Van Nerom, Niels Vandenberk, Ranjan Kumar Singh, Albert Konijnenberg, Steven De Gieter, Daniel Castro-Roa, Anders Barth, Henri De Greve, Frank Sobott, Johan Hofkens, Nikolay Zenkin, Remy Loris, Abel Garcia-Pino
Bacterial protein synthesis is intricately connected to metabolic rate. One of the ways in which bacteria respond to environmental stress is through posttranslational modifications of translation factors. Translation elongation factor Tu (EF-Tu) is methylated and phosphorylated in response to nutrient starvation upon entering stationary phase, and its phosphorylation is a crucial step in the pathway toward sporulation. We analyze how phosphorylation leads to inactivation of Escherichia coli EF-Tu. We provide structural and biophysical evidence that phosphorylation of EF-Tu at T382 acts as an efficient switch that turns off protein synthesis by decoupling nucleotide binding from the EF-Tu conformational cycle...
March 2018: Science Advances
https://www.readbyqxmd.com/read/29531062/ef-tu-and-ef-g-are-activated-by-allosteric-effects
#7
Dibyendu Mondal, Arieh Warshel
Many cellular processes are controlled by GTPases, and gaining quantitative understanding of the activation of such processes has been a major challenge. In particular, it is crucial to obtain reliable free-energy surfaces for the relevant reaction paths both in solution and in GTPases active sites. Here, we revisit the energetics of the activation of EF-G and EF-Tu by the ribosome and explore the nature of the catalysis of the GTPase reaction. The comparison of EF-Tu to EF-G allows us to explore the impact of possible problems with the available structure of EF-Tu...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29459784/2-o-methylation-in-mrna-disrupts-trna-decoding-during-translation-elongation
#8
Junhong Choi, Gabriele Indrisiunaite, Hasan DeMirci, Ka-Weng Ieong, Jinfan Wang, Alexey Petrov, Arjun Prabhakar, Gideon Rechavi, Dan Dominissini, Chuan He, Måns Ehrenberg, Joseph D Puglisi
Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading...
February 19, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29447106/challenges-of-site-specific-selenocysteine-incorporation-into-proteins-by-escherichia-coli
#9
Xian Fu, Dieter Söll, Anastasia Sevostyanova
Selenocysteine (Sec), a rare genetically encoded amino acid with unusual chemical properties, is of great interest for protein engineering. Sec is synthesized on its cognate tRNA (tRNA Sec ) by the concerted action of several enzymes. While all other aminoacyl-tRNAs are delivered to the ribosome by the elongation factor Tu (EF-Tu), Sec-tRNA Sec requires a dedicated factor, SelB. Incorporation of Sec into protein requires recoding of the stop codon UGA aided by a specific mRNA structure, the SECIS element. This unusual biogenesis restricts the use of Sec in recombinant proteins, limiting our ability to study the properties of selenoproteins...
February 15, 2018: RNA Biology
https://www.readbyqxmd.com/read/29444814/plastid-translation-elongation-factor-tu-is-prone-to-heat-induced-aggregation-despite-its-critical-role-in-plant-heat-tolerance
#10
Xifeng Li, Chong Cai, Zhe Wang, Baofang Fan, Cheng Zhu, Zhixiang Chen
Translation elongation factor Tu (EF-Tu) is a conserved GTP-binding protein essential for protein translation in prokaryotes and eukaryotic organelles of mitochondria and plastids. EF-Tu also has a GTP/GDP-independent chaperone activity implicated in heat adaptation. Here, we report that Arabidopsis plastid EF-Tu, Rabe1b, rapidly became insoluble in vitro at a temperature as low as 35{degree sign}, but remained largely soluble in vivo at the elevated temperature. At a temperature above 41{degree sign}C, insolubilization of Rabe1b also occurred in vivo, with more than 90% becoming aggregated in 9 hours at 45{degree sign}C...
February 14, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29439212/oxidation-of-translation-factor-ef-tu-inhibits-the-repair-of-photosystem-ii
#11
Haruhiko Jimbo, Rayakorn Yutthanasirikul, Takanori Nagano, Toru Hisabori, Yukako Hihara, Yoshitaka Nishiyama
The repair of photosystem II (PSII) is particularly sensitive to oxidative stress and the inhibition of repair is associated with oxidative damage to the translational elongation system in the cyanobacterium Synechocystis sp. PCC 6803. However, the molecular mechanism of the inhibition of translational elongation remains to be clarified. In a previous study in vitro, we found that EF-Tu, a translation factor that delivers aminoacyl-tRNA to the ribosome, is inactivated by reactive oxygen species via oxidation of Cys82, a single cysteine residue...
February 8, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29366563/pneumococcal-dna-binding-proteins-released-through-autolysis-induce-the-production-of-proinflammatory-cytokines-via-toll-like-receptor-4
#12
Kosuke Nagai, Hisanori Domon, Tomoki Maekawa, Masataka Oda, Takumi Hiyoshi, Hikaru Tamura, Daisuke Yonezawa, Yoshiaki Arai, Mai Yokoji, Koichi Tabeta, Rie Habuka, Akihiko Saitoh, Masaya Yamaguchi, Shigetada Kawabata, Yutaka Terao
Streptococcus pneumoniae is a leading cause of bacterial pneumonia. Our previous study suggested that S. pneumoniae autolysis-dependently releases intracellular pneumolysin, which subsequently leads to lung injury. In this study, we hypothesized that pneumococcal autolysis induces the leakage of additional intracellular molecules that could increase the pathogenicity of S. pneumoniae. Liquid chromatography tandem-mass spectrometry analysis identified that chaperone protein DnaK, elongation factor Tu (EF-Tu), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were released with pneumococcal DNA by autolysis...
March 2018: Cellular Immunology
https://www.readbyqxmd.com/read/29339430/simultaneous-binding-of-multiple-ef-tu-copies-to-translating-ribosomes-in-live-escherichia-coli
#13
Mainak Mustafi, James C Weisshaar
In bacteria, elongation factor Tu is a translational cofactor that forms ternary complexes with aminoacyl-tRNA (aa-tRNA) and GTP. Binding of a ternary complex to one of four flexible L7/L12 units on the ribosome tethers a charged tRNA in close proximity to the ribosomal A site. Two sequential tests for a match between the aa-tRNA anticodon and the current mRNA codon then follow. Because one elongation cycle can occur in as little as 50 ms and the vast majority of aa-tRNA copies are not cognate with the current mRNA codon, this testing must occur rapidly...
January 16, 2018: MBio
https://www.readbyqxmd.com/read/29284022/a-transcriptomics-approach-uncovers-novel-roles-for-poly-adp-ribosyl-ation-in-the-basal-defense-response-in-arabidopsis-thaliana
#14
Amy G Briggs, Lori C Adams-Phillips, Brian D Keppler, Sophia G Zebell, Kyle C Arend, April A Apfelbaum, Joshua A Smith, Andrew F Bent
Pharmacological inhibition of poly(ADP-ribose) polymerase (PARP) or loss of Arabidopsis thaliana PARG1 (poly(ADP-ribose) glycohydrolase) disrupt a subset of plant defenses. In the present study we examined the impact of altered poly(ADP-ribosyl)ation on early gene expression induced by the microbe-associate molecular patterns (MAMPs) flagellin (flg22) and EF-Tu (elf18). Stringent statistical analyses and filtering identified 178 genes having MAMP-induced mRNA abundance patterns that were altered by either PARP inhibitor 3-aminobenzamide (3AB) or PARG1 knockout...
2017: PloS One
https://www.readbyqxmd.com/read/29276038/structural-and-dynamics-comparison-of-thermostability-in-ancient-modern-and-consensus-elongation-factor-tus
#15
C Denise Okafor, Manish C Pathak, Crystal E Fagan, Nicholas C Bauer, Megan F Cole, Eric A Gaucher, Eric A Ortlund
Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into the mechanisms by which proteins become more stable, we use structural and dynamic analyses to compare two popular approaches, ancestral sequence reconstruction (ASR) and the consensus method, used to generate thermostable variants of Elongation Factor Thermo-unstable (EF-Tu)...
January 2, 2018: Structure
https://www.readbyqxmd.com/read/29250804/nonredundant-functions-of-arabidopsis-lecrk-v-2-and-lecrk-vii-1-in-controlling-stomatal-immunity-and-jasmonate-mediated-stomatal-closure
#16
Shweta Yekondi, Fu-Chun Liang, Eiji Okuma, Amandine Radziejwoski, Hsien-Wei Mai, Swadhin Swain, Prashant Singh, Mathieu Gauthier, Hsiao-Chiao Chien, Yoshiyuki Murata, Laurent Zimmerli
Stomatal immunity restricts bacterial entry to leaves through the recognition of microbe-associated molecular patterns (MAMPs) by pattern-recognition receptors (PRRs) and downstream abscisic acid and salicylic acid signaling. Through a reverse genetics approach, we characterized the function of the L-type lectin receptor kinase-V.2 (LecRK-V.2) and -VII.1 (LecRK-VII.1). Analyses of interactions with the PRR FLAGELLIN SENSING2 (FLS2) were performed by co-immunoprecipitation and bimolecular fluorescence complementation and whole-cell patch-clamp analyses were used to evaluate guard cell Ca2+ -permeable cation channels...
April 2018: New Phytologist
https://www.readbyqxmd.com/read/29235176/roles-of-elusive-translational-gtpases-come-to-light-and-inform-on-the-process-of-ribosome-biogenesis-in-bacteria
#17
REVIEW
Michelle R Gibbs, Kurt Fredrick
Protein synthesis relies on several translational GTPases (trGTPases), related proteins that couple the hydrolysis of GTP to specific molecular events on the ribosome. Most bacterial trGTPases, including IF2, EF-Tu, EF-G and RF3, play well-known roles in translation. The cellular functions of LepA (also termed EF4) and BipA (also termed TypA), conversely, have remained enigmatic. Recent studies provide compelling in vivo evidence that LepA and BipA function in biogenesis of the 30S and 50S subunit respectively...
February 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29155943/logical-engineering-of-d-arm-and-t-stem-of-trna-that-enhances-d-amino-acid-incorporation
#18
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...
December 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29058676/model-based-local-density-sharpening-of-cryo-em-maps
#19
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
#20
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...
November 14, 2017: Biochemistry
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