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Protein Biosynthesis (6):
Recent article
Protein Biosynthesis
Abstract
We developed a nuclear magnetic resonance approach that enabled direct detection of structural elements within the intact leader (712-nucleotide dimer) that are critical for genome packaging. Residues spanning the gag start codon (AUG) form a hairpin in the monomeric leader and base pair with residu...
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PMID: 21998393
PDF is available here.
PDF is available here.
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Abstract
We identify a previously unknown target of POA as the ribosomal protein S1 (RpsA), a vital protein involved in protein translation and the ribosome-sparing process of trans-translation. Three PZA-resistant clinical isolates without pncA mutation harbored RpsA mutations. RpsA overexpression conferred...
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PMID: 21835980
PDF is available here.
PDF is available here.
Abstract
We functionally characterized the DExD/H box adenosine triphosphatase (ATPase) Dhh1, a critical regulator of the cytoplasmic fate of mRNAs. Using mRNA tethering experiments in yeast, we showed that Dhh1 was sufficient to move an mRNA from an active state to translational repression. In actively divi...
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PMID: 21844211
PDF is available here.
PDF is available here.
Abstract
We here isolated N-terminal peptides of a Saccharomyces cerevisiae proteome and analyzed both annotated and alternative TIS. We analyzed this N-terminome of S. cerevisiae which resulted in the identification of 650 unique N-terminal peptides corresponding to database annotated TIS. Furthermore, 56 u...
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PMID: 21619078
PDF is available here.
PDF is available here.
Abstract
Using structures of mRNP of different cell localization isolated from plants infected by minus-genomecurly potato dwarfness virus (CPDV), it was established that synthesis of virus proteins in vitro is mainly realized on membrane-related and free polysomal mRNP capable to direct synthesis of proteins...
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PMID: 21809689
PDF is available here.
PDF is available here.
Abstract
We show that SXL binding downstream of a short uORF imposes a strong negative effect on major reading frame translation. The underlying mechanism involves increasing initiation of scanning ribosomes at the uORF and augmenting its impediment to downstream translation. Our analyses reveal that SXL exe...
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PMID: 21663794
PDF is available here.
PDF is available here.
Abstract
Yeast ribosomal protein L11 is positioned at the intersubunit cleft of the large subunit central protuberance, forming an intersubunit bridge with the small subunit protein S18. Mutants were engineered in the central core region of L11 which interacts with Helix 84 of the 25S rRNA. N...
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PMID: 21519857
PDF is available here.
PDF is available here.
Abstract
We extensively characterize alternative first exons of the mouse GR to reveal homology to the rat and human. We further find that, although most promoters are broadly expressed in various tissues, transcription of individual promoters can be differentially regulated by growth factor- and depolarizat...
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PMID: 21527501
PDF is available here.
PDF is available here.
Abstract
Aging cells accumulate damaged and misfolded proteins through a functional decline in their protein homeostasis (proteostasis) machinery, leading to reduced cellular viability and the development of protein misfolding diseases such as Alzheimer's and Huntington's. Metabolic signaling...
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PMID: 21441594
PDF is available here.
PDF is available here.
Cell Host & Microbe (9)4 2011
Abstract
We show that the Leishmania protease GP63 cleaves the mammalian/mechanistic target of rapamycin (mTOR), a serine/threonine kinase that regulates the translational repressor 4E-BP1. mTOR cleavage results in the inhibition of mTOR complex 1 (mTORC1) and concomitant activation of 4E-BP1 to promote Leis...
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PMID: 21501832
PDF is available here.
PDF is available here.
Abstract
We review modern developments in genomics and systems biology that have revolutionized our understanding of the multiple means by which translation is regulated. We suggest new means to model the process of translation in a richer framework that will incorporate information about gene sequences, the...
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PMID: 21487400
PDF is available here.
PDF is available here.
Abstract
In this study, a new technique that controls individual cell orientation using nanofiber meshes within three-dimensional (3D) hydrogels is reported. Highly aligned and fragile electrospun nanofibers (average diameter 500 nm) were manufactured into portable and handleable meshes with...
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PMID: 21272664
PDF is available here.
PDF is available here.
Abstract
We show that although MSCs effectively engraft in AMI tissue, this engraftment leads to downregulation of CP expression in the implanted MSCs. We also found that pretransplantation cardiac specification of MSCs by exposure of the cells to transforming growth factor beta 1 (TGF-β1) led to sustained...
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PMID: 20666606
PDF is available here.
PDF is available here.
Abstract
We characterized two efficiency phenotypes: high- vs. low-performers associated with the two AATn genotypes, AAT12/14 vs. AAT12/13. The findings suggest that AATn polymorphism modifies CNR1 translation, indicating a different modulation of CB1....
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PMID: 21396980
PDF is available here.
PDF is available here.
Abstract
We present an overview of the main results arrived at by the application of single-molecule methods to the study of the main machines of the central dogma.
Copyright © 2011 Elsevier Inc. All rights reserved....
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PMID: 21335233
PDF is available here.
PDF is available here.
Abstract
We report mutants of a novel Drosophila gene twenty-four (tyf) that show weak behavioural rhythms. Weak rhythms are accompanied by marked reductions in the levels of the clock protein Period (PER) as well as more modest effects on Timeless (TIM). Nonetheless, PER induction in pacemaker neurons can r...
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PMID: 21331043
PDF is available here.
PDF is available here.
Proteomics (11)4 2011
Abstract
The simultaneous analysis of a wide array of proteins may provide valuable information on the activation and suppression of cellular systems at different stages of the exposure-disease continuum. In this review, results of proteomic studies in the field of toxicology are covered, foc...
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PMID: 21246732
PDF is available here.
PDF is available here.
Abstract
We have compared the repeatability, susceptibility to contamination from off-target cell-types, and evidence for stress-responsive gene expression of five different purification methods--Laser Capture Microdissection (LCM), Translating Ribosome Affinity Purification (TRAP), Immunopanning (PAN), Fluo...
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PMID: 21304595
PDF is available here.
PDF is available here.
Abstract
Rubisco (ribulose-1, 5-bisphosphate carboxylase/oxygenase), a key enzyme of photosynthetic CO(2) fixation, is one of the most abundant proteins in both higher plants and algae. In this study, the differential expression of Rubisco in sporophytes and gametophytes of four seaweed species--Porphyra yezo...
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PMID: 21283730
PDF is available here.
PDF is available here.
Abstract
We previously showed that, similarly with fear memories, reactivated spatial memory undergoes reconsolidation in the Morris water maze. However, the underlying molecular mechanisms by which reactivated spatial memory is destabilized and restabilized remain poorly understood. In this study, we invest...
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PMID: 21314917
PDF is available here.
PDF is available here.
Abstract
Memory consolidation is a process to stabilize short-term memory, generating long-term memory. A critical biochemical feature of memory consolidation is a requirement for gene expression. Previous studies have shown that fear memories are consolidated through the activation of gene expression in the...
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PMID: 21244716
PDF is available here.
PDF is available here.
Abstract
We demonstrate that transgenic mice expressing EGFP transcripts with long CAG repeats in the 3' untranslated region develop pathogenic features. Expression of the transgene was directed to the muscle in order to compare the resulting phenotype to that caused by the CUG expansion, as occurs in myoton...
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PMID: 21283659
PDF is available here.
PDF is available here.
Abstract
We report a thorough comparative study on 203 well-selected bacterial species, which strongly suggest that the previous conclusion is likely an illusion. Firstly, the previous study did not preclude species that are suffering weak or no selection pressures on their codon usages. For these species, a...
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PMID: 21829489
PDF is available here.
PDF is available here.
Abstract
Neurons are highly polarized cells with extensive sub-cellular compartmentalization to accommodate diverse local needs. Information flows between the pre-synaptic (axon) and post-synaptic (dendrite) compartments, as well as between the soma and the nerve termini. It is critical that a neuron control...
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PMID: 21116543
PDF is available here.
PDF is available here.
Abstract
Diet and obesity are important risk factors for cancer development. Many studies have suggested an important role for several dietary nutrients in the progression and development of breast cancer. However, few studies have specifically addressed the role of components of a Western diet as important f...
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PMID: 21224077
PDF is available here.
PDF is available here.
Abstract
We have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for ∼5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark con...
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PMID: 21364985
PDF is available here.
PDF is available here.
Abstract
Abstract
Yeast ribosomal proteins L11 and S18 form a dynamic intersubunit interaction called the B1b/c bridge. Recent high resolution images of the ribosome have enabled targeting of specific residues in this bridge to address how distantly separated regions within the large and small subunit...
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PMID: 21625514
PDF is available here.
PDF is available here.
Abstract
Our results support the model that the QS sRNAs bind to the 5' untranslated region of multiple mRNAs and alter the fate of one in a positive manner and several others in a negative manner. This mechanism ensures the proper timing of the QS response, which includes the expression of traits critical f...
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PMID: 21031313
PDF is available here.
PDF is available here.
Abstract
We have described in this chapter the methods used in our laboratory for investigations of the import of nuclear-encoded proteins across the chloroplast envelope membranes, and for their further delivery into or across the thylakoid membrane by one of the four distinct pathways....
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PMID: 20960128
PDF is available here.
PDF is available here.
Development (138)3 2011
Abstract
We observed that unlike other mRNAs, synthetic nanos1 RNA translates very poorly if at all after injection into Xenopus oocytes. The current model of simple sequestration of nanos1 within germinal granules is insufficient to explain this observation and suggests that a second level of repression mus...
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PMID: 21205802
PDF is available here.
PDF is available here.
Abstract
We want to express and test the hypothesis that the NO is necessary both for erasure and development of memory. In our experiments in terrestrial snail Helix we tested the idea that NO besides well shown participation in memory development is involved in erasure/lockout of memory during relearning a...
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PMID: 21861383
PDF is available here.
PDF is available here.
Abstract
We use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 3...
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PMID: 21124459
PDF is available here.
PDF is available here.
Abstract
We found in this study that blockade of the interaction of p53 and MDM2 by the MDM2 antagonist nutlin-3 in melanoma cells did not induce apoptosis, even though it upregulated p53 and its proapoptotic targets. Nevertheless, nutlin-3 enhanced TRAIL-induced apoptosis as a result of p53-mediated upregul...
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PMID: 21159614
PDF is available here.
PDF is available here.
EMBO Journal (29)23 2010
Abstract
We find that mTORC2 can colocalize with actively translating ribosomes and can stably interact with rpL23a, a large ribosomal subunit protein present at the tunnel exit. Exclusively during translation of Akt, mTORC2 mediates phosphorylation of the nascent polypeptide at the turn motif (TM) site, Thr...
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PMID: 21045808
PDF is available here.
PDF is available here.
Abstract
We show that a West Nile virus (WNV) mutant (E218A) that lacks 2'-O MTase activity was attenuated in wild-type primary cells and mice but was pathogenic in the absence of type I interferon (IFN) signalling. 2'-O methylation of viral RNA did not affect IFN induction in WNV-infected fibroblasts but in...
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PMID: 21085181
PDF is available here.
PDF is available here.
Abstract
We have shown, that PPARγ activates ABCA1 gene transcription in human hepatoma cells HepG2 through increasing of LXRβ binding with promoter region of ABCA1 gene. Treatment of HepG2 cells with PPARγ agonist GW1929 leads to dissociation of LXRβ from ABCA1/LXRβ complex and to nuclear translocation...
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PMID: 20951680
PDF is available here.
PDF is available here.
Abstract
We investigated the interaction between evodiamine and the aryl hydrocarbon receptor (AhR). Molecular modeling results revealed that evodiamine directly interacted with the AhR. Cytosolic receptor binding assay also provided the evidence that evodiamine could interact with the AhR with the K(i) valu...
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PMID: 20888792
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)45 2010
Abstract
These results demonstrate a new hierarchical phosphorylation for 4E-BP1 regulation in which Thr(69) is phosphorylated first followed by Thr(36)/Thr(45) phosphorylation, and Ser(64) is phosphorylated last. Thr(69) phosphorylation alone allows binding to eIF4E, and subsequent Thr(36)/Thr(45) phosphory...
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PMID: 20736160
PDF is available here.
PDF is available here.
Nature Methods (7)11 2010
Abstract
We introduce a quantitative proteomics approach to sort out non-cell-autonomous proteins synthesized by other cells or intracellular pathogens. Our approach combines stable-isotope labeling of amino acids in cell culture (SILAC), high-purity cell sorting and bioinformatics analysis to identify the r...
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PMID: 20935649
PDF is available here.
PDF is available here.
Molecular Therapy (18)11 2010
Abstract
We report here that growth and cytotoxicity of the prototype oncolytic poliovirus (PV), PVSRIPO, in glioblastoma multiforme (GBM) is promoted by mitogen-activated protein kinases (MAPKs) converging on the MAPK signal-integrating kinase 1 (Mnk1) and its primary substrate, the eukaryotic initiation fa...
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PMID: 20648000
PDF is available here.
PDF is available here.
Molecular Therapy (18)11 2010
Abstract
We asked whether these results were likely to translate to patients. To understand to what extent preexisting anti-AAV8 antibodies could impede AAV8-mediated liver transduction in primates, commonly preexposed to AAV, we quantified the effects of preexisting antibodies on liver transduction and subs...
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PMID: 20736932
PDF is available here.
PDF is available here.
Development (137)22 2010
Abstract
We report that although Nv nanos (Nv-nos) has a conserved function in embryonic patterning through translational repression of hb, the timing and mechanisms of this repression are significantly delayed in the wasp compared with the fly. This delay in Nv-nos function appears to be related to the dyna...
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PMID: 20929949
PDF is available here.
PDF is available here.
EMBO Journal (29)21 2010
Abstract
We analyse the speed and accuracy of the decoding step under conditions reproducing the high speed of translation in vivo. We show that error frequency is close to 10⁻³, consistent with the values measured in vivo. Selectivity is predominantly due to the differences in k(cat) values for cognate a...
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PMID: 20842102
PDF is available here.
PDF is available here.
Abstract
These results illustrate the great progress that has been made in the HCV field and how this knowledge can be used to devise innovative strategies to counteract this pathogen.
© Thieme Medical Publishers....
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PMID: 20960374
PDF is available here.
PDF is available here.
EMBO Journal (29)21 2010
Abstract
Tethered hydroxyl-radical probing has been used to determine the orientation of binding of polypyrimidine tract-binding protein (PTB) to the poliovirus type 1 (Mahoney) (PV-1(M)) internal ribosome entry site/segment (IRES)-the question of which RNA-binding domain (RBD) binds to which sites on the IR...
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PMID: 20859255
PDF is available here.
PDF is available here.
Biochemical Journal (432)1 2010
Abstract
We show that the A chain of ricin, the well-known plant RIP (ribosome-inactivating protein), interacts with PMN (Kd=10⁻⁹ M; 2×10⁵ binding sites) competing for the same receptor that recognizes Stx, whereas diphtheria toxin and several agonists of TLRs (Toll-like receptors) or the mannose rece...
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PMID: 20809900
PDF is available here.
PDF is available here.
Abstract
We show that Dom34:Hbs1 interacts with the ribosome to promote subunit dissociation and peptidyl-tRNA drop-off. Our data further indicate that these recycling activities are shared by the homologous translation termination factor complex eRF1:eRF3, suggesting a common ancestral function. Because Dom...
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PMID: 20947765
PDF is available here.
PDF is available here.
Abstract
We report the characterization of the sup-26 gene, which regulates sex determination in the soma and encodes an RNA recognition motif (RRM)-containing protein. We show that SUP-26 regulates the level of the TRA-2 protein through TGE in vivo and binds directly to TGE in vitro through its RRM domain....
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PMID: 20921392
PDF is available here.
PDF is available here.
New England Journal of Medicine (363)15 2010
Abstract
We report on delivery of a functional dystrophin transgene to skeletal muscle in six patients with Duchenne's muscular dystrophy. Dystrophin-specific T cells were detected after treatment, providing evidence of transgene expression even when the functional protein was not visualized in skeletal musc...
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PMID: 20925545
PDF is available here.
PDF is available here.
Molecular BioSystems (6)10 2010
Abstract
We employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls....
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PMID: 20544124
PDF is available here.
PDF is available here.
Behavioral Neuroscience (124)5 2010
Abstract
We demonstrate that habituation to an antifeedant compound (quinine) persists through the moult between larval instars. As an indirect test of whether the memory was protein synthesis-dependent, we tested whether disrupting protein synthesis would block memory reconsolidation after a reminder. The r...
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PMID: 20939670
PDF is available here.
PDF is available here.
Abstract
I small heat shock protein (sHSP-CI) genes were found to be selectively induced by L-azetidine-2-carboxylic acid (AZC) on chromosome 3 but not chromosome 1. Here it is shown that a novel cis-responsive element contributed to the differential regulation. By serial deletion and computational analysis,...
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PMID: 20643810
PDF is available here.
PDF is available here.
Abstract
We investigate the role of leptin on articular cartilage in vivo in this study. Recombinant rat leptin (100 μg) was injected into the knee joints of rats, 48 h later, messenger RNA (mRNA) expression and protein levels of basic fibroblast growth factor (bFGF), vascular endothelial growth factor (VEG...
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PMID: 19876764
PDF is available here.
PDF is available here.
Abstract
We show that the Saccharomyces cerevisiae Ltn1 RING-domain-type E3 ubiquitin ligase acts in the quality control of non-stop proteins, in a process that is mechanistically distinct but conceptually analogous to that performed by ssrA: Ltn1 is predominantly associated with ribosomes, and it marks nasc...
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PMID: 20835226
PDF is available here.
PDF is available here.
Abstract
We computationally examined the protein sequences of all major taxonomical groups represented in the Swiss-Prot database, and evaluated the preference of each group to specific amino acids at the positions directly following the initial Met. The results indicate that there is a species-specific pref...
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PMID: 20970746
PDF is available here.
PDF is available here.
Molecular Cell (39)4 2010
Abstract
We have mapped individual ribosomes in electron tomograms of intact human cells by template matching and determined the average structure of the ribosome in situ. Characteristic features of active ribosomes in the cellular environment were assigned to the tRNA channel, elongation factors, and additi...
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PMID: 20797628
PDF is available here.
PDF is available here.
Genes & Development (24)17 2010
Abstract
She2p is an RNA-binding protein that recognizes a zipcode on specific mRNAs necessary for the assembly of a protein complex that localizes them to the yeast bud tip. In this issue of Genes & Development, Shen and colleagues (pp. 1914-1926) demonstrate that She2p associates with RNAPII globally, but t...
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PMID: 20810644
PDF is available here.
PDF is available here.
Journal of Dairy Science (93)9 2010
Abstract
We determined the mRNA and protein expression of DNMT1 in Jurkat T-leukemia cells, after incubation with Lfcin B, by real-time quantitative reverse transcription PCR and Western blot analysis. The results of real-time quantitative reverse transcription PCR showed that DNMT1 expression in Jurkat T-le...
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PMID: 20723665
PDF is available here.
PDF is available here.
Journal of Dairy Science (93)9 2010
Abstract
Our results revealed changes in intestinal growth after soy protein feeding that were associated with effects on intestinal RNA and protein synthesis but that were not ameliorated by AA supplementation.
Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights rese...
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PMID: 20723691
PDF is available here.
PDF is available here.