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Cotranslation

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https://www.readbyqxmd.com/read/29286490/a-facile-protocol-to-generate-site-specifically-acetylated-proteins-in-escherichia-coli
#1
Sumana Venkat, Caroline Gregory, Kexin Meng, Qinglei Gan, Chenguang Fan
Post-translational modifications that occur at specific positions of proteins have been shown to play important roles in a variety of cellular processes. Among them, reversible lysine acetylation is one of the most widely distributed in all domains of life. Although numerous mass spectrometry-based acetylome studies have been performed, further characterization of these putative acetylation targets has been limited. One possible reason is that it is difficult to generate purely acetylated proteins at desired positions by most classic biochemical approaches...
December 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29282902/construction-of-green-fluorescence-protein-mutant-to-monitor-stt3b-dependent-n-glycosylation
#2
Toshihiko Kitajima, Wei Xue, Yi-Shi Liu, Chun-Di Wang, Si-Si Liu, Morihisa Fujita, Xiao-Dong Gao
Oligosaccharyltransferases (OSTs) mediate the en bloc transfer of N-glycan intermediates onto the asparagine residue in glycosylation sequons (N-X-S/T, X≠P). These enzymes are typically heteromeric complexes composed of several membrane-associated subunits, in which STT3 is highly conserved as a catalytic core. Metazoan organisms encode two STT3 genes (STT3A and STT3B) in their genome, resulting in the formation of at least two distinct OST isoforms consisting of shared subunits and complex specific subunits...
December 28, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29226470/photo-crosslinkable-unnatural-amino-acids-enable-facile-synthesis-of-thermoresponsive-nano-to-microgels-of-intrinsically-disordered-polypeptides
#3
Simone A Costa, Joseph R Simon, Miriam Amiram, Lei Tang, Stefan Zauscher, Eric M Brustad, Farren J Isaacs, Ashutosh Chilkoti
Hydrogel particles are versatile materials that provide exquisite, tunable control over the sequestration and delivery of materials in pharmaceutics, tissue engineering, and photonics. The favorable properties of hydrogel particles depend largely on their size, and particles ranging from nanometers to micrometers are used in different applications. Previous studies have only successfully fabricated these particles in one specific size regime and required a variety of materials and fabrication methods. A simple yet powerful system is developed to easily tune the size of polypeptide-based, thermoresponsive hydrogel particles, from the nano- to microscale, using a single starting material...
December 11, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29203677/dynamics-of-translation-can-determine-the-spatial-organization-of-membrane-bound-proteins-and-their-mrna
#4
Elgin Korkmazhan, Hamid Teimouri, Neil Peterman, Erel Levine
Unlike most macromolecules that are homogeneously distributed in the bacterial cell, mRNAs that encode inner-membrane proteins can be concentrated near the inner membrane. Cotranslational insertion of the nascent peptide into the membrane brings the translating ribosome and the mRNA close to the membrane. This suggests that kinetic properties of translation can determine the spatial organization of these mRNAs and proteins, which can be modulated through posttranscriptional regulation. Here we use a simple stochastic model of translation to characterize the effect of mRNA properties on the dynamics and statistics of its spatial distribution...
December 4, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29183994/translation-efficiency-is-maintained-at-elevated-temperature-in-e-coli
#5
Gareth J Morgan, David H Burkhardt, Jeffery W Kelly, Evan T Powers
Cellular protein levels are dictated by the balance between gene transcription, mRNA translation and protein degradation, among other factors. Translation requires the interplay of several RNA hybridization processes, which are expected to be temperature sensitive. We used ribosome profiling to monitor translation in E. coli at 30 °C and investigate how this changes after 10-20 minutes of heat shock at 42 °C. Translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat shock response transcriptional program at 30 °C by overexpressing the heat shock sigma factor encoded by the rpoH gene...
November 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29136098/sequential-search-leads-to-faster-more-efficient-fragment-based-de-novo-protein-structure-prediction
#6
Saulo H P de Oliveira, Eleanor C Law, Jiye Shi, Charlotte M Deane
Motivation: Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. Results: We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29080176/analysis-of-cotranslational-polyamine-sensing-during-decoding-of-odc-antizyme-mrna
#7
R Palanimurugan, Daniela Gödderz, Leo Kurian, R Jürgen Dohmen
Polyamines are essential poly-cations with vital functions in all cellular systems. Their levels are controlled by intricate regulatory feedback mechanisms. Abnormally high levels of polyamines have been linked to cancer. A rate-limiting enzyme in the biosynthesis of polyamines in fungi and higher eukaryotes is ornithine-decarboxylase (ODC). Its levels are largely controlled posttranslationally via ubiquitin-independent degradation mediated by ODC antizyme (OAZ). The latter is a critical polyamine sensor in a feedback control mechanism that adjusts cellular polyamine levels...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29073068/evidence-of-evolutionary-selection-for-cotranslational-folding
#8
William M Jacobs, Eugene I Shakhnovich
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from cotranslational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for cotranslational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29057042/apratoxin-s10-a-dual-inhibitor-of-angiogenesis-and-cancer-cell-growth-to-treat-highly-vascularized-tumors
#9
Weijing Cai, Qi-Yin Chen, Long H Dang, Hendrik Luesch
Renal, hepatocellular, and neuroendocrine carcinomas are known as highly vascularized tumors. Although vascular endothelial growth factor A (VEGF-A)-targeted therapies have shown efficacy in the treatment of these cancers, drug resistance is a major concern and might be mediated by interleukin 6 (IL-6). Furthermore, upon antiangiogenic drug exposure, tumor cells may adapt to survive in a vascular-independent manner. Apratoxins are potent marine-derived cytotoxic in vivo-active agents, preventing cotranslational translocation in the secretory pathway, and show promise to overcome resistance by targeting angiogenesis and tumor growth simultaneously...
October 12, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29038496/the-hsp70-homolog-ssb-affects-ribosome-biogenesis-via-the-torc1-sch9-signaling-pathway
#10
Kaivalya Mudholkar, Edith Fitzke, Claudia Prinz, Matthias P Mayer, Sabine Rospert
The Hsp70 Ssb serves a dual role in de novo protein folding and ribosome biogenesis; however, the mechanism by which Ssb affects ribosome production is unclear. Here we establish that Ssb is causally linked to the regulation of ribosome biogenesis via the TORC1-Sch9 signaling pathway. Ssb is bound to Sch9 posttranslationally and required for the TORC1-dependent phosphorylation of Sch9 at T737. Also, Sch9 lacking phosphorylation at T737 displays significantly reduced kinase activity with respect to targets involved in the regulation of ribosome biogenesis...
October 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28972538/mutations-in-signal-recognition-particle-srp54-cause-syndromic-neutropenia-with-shwachman-diamond-like-features
#11
Raphael Carapito, Martina Konantz, Catherine Paillard, Zhichao Miao, Angélique Pichot, Magalie S Leduc, Yaping Yang, Katie L Bergstrom, Donald H Mahoney, Deborah L Shardy, Ghada Alsaleh, Lydie Naegely, Aline Kolmer, Nicodème Paul, Antoine Hanauer, Véronique Rolli, Joëlle S Müller, Elisa Alghisi, Loïc Sauteur, Cécile Macquin, Aurore Morlon, Consuelo Sebastia Sancho, Patrizia Amati-Bonneau, Vincent Procaccio, Anne-Laure Mosca-Boidron, Nathalie Marle, Naël Osmani, Olivier Lefebvre, Jacky G Goetz, Sule Unal, Nurten A Akarsu, Mirjana Radosavljevic, Marie-Pierre Chenard, Fanny Rialland, Audrey Grain, Marie-Christine Béné, Marion Eveillard, Marie Vincent, Julien Guy, Laurence Faivre, Christel Thauvin-Robinet, Julien Thevenon, Kasiani Myers, Mark D Fleming, Akiko Shimamura, Elodie Bottollier-Lemallaz, Eric Westhof, Claudia Lengerke, Bertrand Isidor, Seiamak Bahram
Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa)...
October 3, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28957655/analysis-of-ribosome-stalling-and-translation-elongation-dynamics-by-deep-learning
#12
Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng
Ribosome stalling is manifested by the local accumulation of ribosomes at specific codon positions of mRNAs. Here, we present ROSE, a deep learning framework to analyze high-throughput ribosome profiling data and estimate the probability of a ribosome stalling event occurring at each genomic location. Extensive validation tests on independent data demonstrated that ROSE possessed higher prediction accuracy than conventional prediction models, with an increase in the area under the receiver operating characteristic curve by up to 18...
September 27, 2017: Cell Systems
https://www.readbyqxmd.com/read/28946879/contribution-of-single-amino-acid-and-codon-substitutions-to-the-production-and-secretion-of-a-lipase-by-bacillus-subtilis
#13
Pia Skoczinski, Kristina Volkenborn, Alexander Fulton, Anuseema Bhadauriya, Christina Nutschel, Holger Gohlke, Andreas Knapp, Karl-Erich Jaeger
BACKGROUND: Bacillus subtilis produces and secretes proteins in amounts of up to 20 g/l under optimal conditions. However, protein production can be challenging if transcription and cotranslational secretion are negatively affected, or the target protein is degraded by extracellular proteases. This study aims at elucidating the influence of a target protein on its own production by a systematic mutational analysis of the homologous B. subtilis model protein lipase A (LipA). We have covered the full natural diversity of single amino acid substitutions at 155 positions of LipA by site saturation mutagenesis excluding only highly conserved residues and qualitatively and quantitatively screened about 30,000 clones for extracellular LipA production...
September 25, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28928132/seca-mediates-cotranslational-targeting-and-translocation-of-an-inner-membrane-protein
#14
Shuai Wang, Chien-I Yang, Shu-Ou Shan
Protein targeting to the bacterial plasma membrane was generally thought to occur via two major pathways: cotranslational targeting by signal recognition particle (SRP) and posttranslational targeting by SecA and SecB. Recently, SecA was found to also bind ribosomes near the nascent polypeptide exit tunnel, but the function of this SecA-ribosome contact remains unclear. In this study, we show that SecA cotranslationally recognizes the nascent chain of an inner membrane protein, RodZ, with high affinity and specificity...
November 6, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28924459/genetic-code-optimization-for-cotranslational-protein-folding-codon-directional-asymmetry-correlates-with-antiparallel-betasheets-trna-synthetase-classes
#15
Hervé Seligmann, Ganesh Warthi
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28917045/radioactive-75-se-labeling-and-detection-of-selenoproteins
#16
Sun Hee Yim, Ryuta Tobe, Anton A Turanov, Bradley A Carlson
The trace element selenium (Se) is incorporated into proteins as the amino acid selenocysteine (Sec), which is cotranslationally inserted into specific proteins in response to a UGA codon. Proteins containing Sec at these specific positions are called selenoproteins. Most selenoproteins function as oxidoreductases, while some serve other important functions. There are 25 known selenoprotein genes in humans and 24 in mice. The use of Sec allows selenoproteins to be detected by a convenient method involving metabolic labeling with (75)Se...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28865429/a-new-and-updated-resource-for-codon-usage-tables
#17
John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V Santana-Quintero, Upendra Katneni, Vahan Simonyan, Chava Kimchi-Sarfaty
BACKGROUND: Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression...
September 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28853924/regulation-by-3-untranslated-regions
#18
Christine Mayr
3'-untranslated regions (3'-UTRs) are the noncoding parts of mRNAs. Compared to yeast, in humans, median 3'-UTR length has expanded approximately tenfold alongside an increased generation of alternative 3'-UTR isoforms. In contrast, the number of coding genes, as well as coding region length, has remained similar. This suggests an important role for 3'-UTRs in the biology of higher organisms. 3'-UTRs are best known to regulate diverse fates of mRNAs, including degradation, translation, and localization, but they can also function like long noncoding or small RNAs, as has been shown for whole 3'-UTRs as well as for cleaved fragments...
August 30, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28750053/comprehensive-structural-analysis-of-designed-incomplete-polypeptide-chains-of-the-replicase-nonstructural-protein-1-from-the-severe-acute-respiratory-syndrome-coronavirus
#19
Leonardo Vazquez, Luis Mauricio Trambaioli da Rocha E Lima, Marcius da Silva Almeida
The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures...
2017: PloS One
https://www.readbyqxmd.com/read/28713376/myristoylation-an-important-protein-modification-in-the-immune-response
#20
REVIEW
Daniel Ikenna Udenwobele, Ruey-Chyi Su, Sara V Good, Terry Blake Ball, Shailly Varma Shrivastav, Anuraag Shrivastav
Protein N-myristoylation is a cotranslational lipidic modification specific to the alpha-amino group of an N-terminal glycine residue of many eukaryotic and viral proteins. The ubiquitous eukaryotic enzyme, N-myristoyltransferase, catalyzes the myristoylation process. Precisely, attachment of a myristoyl group increases specific protein-protein interactions leading to subcellular localization of myristoylated proteins with its signaling partners. The birth of the field of myristoylation, a little over three decades ago, has led to the understanding of the significance of protein myristoylation in regulating cellular signaling pathways in several biological processes especially in carcinogenesis and more recently immune function...
2017: Frontiers in Immunology
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