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Encyclopedia of Agriculture and Food Systems (2015)
Florian Eggenhofer et al.
Nucleic acids research, 41(Web Server issue), W499-W503 (2013-05-04)
A standard method for the identification of novel non-coding RNAs is homology search by covariance models. Covariance models are constructed for specific RNA families with common sequence and structure (e.g. transfer RNAs). Currently, there are models for 2208 families available
Jin Chen et al.
Nature structural & molecular biology, 20(6), 718-727 (2013-04-30)
During translation elongation, the ribosome compositional factors elongation factor G (EF-G; encoded by fusA) and tRNA alternately bind to the ribosome to direct protein synthesis and regulate the conformation of the ribosome. Here, we use single-molecule fluorescence with zero-mode waveguides
Stefan Klumpp et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(42), 16754-16759 (2013-10-02)
Bacterial growth is crucially dependent on protein synthesis and thus on the cellular abundance of ribosomes and related proteins. Here, we show that the slow diffusion of the bulky tRNA complexes in the crowded cytoplasm imposes a physical limit on
Changsun Choi et al.
Methods in molecular biology (Clifton, N.J.), 326, 173-188 (2006-06-20)
In this chapter, we describe a simple and relatively rapid technique for detecting low-abundance slug mRNA in cultured cells. The procedure uses nonradioactive digoxigenin-labeled RNA probes that are more sensitive than deoxyribonucleic probes and simpler to detect than radioactively labeled
Tanja Kalstrup et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(20), 8272-8277 (2013-05-01)
Atomic-scale models on the gating mechanism of voltage-gated potassium channels (Kv) are based on linear interpolations between static structures of their initial and final state derived from crystallography and molecular dynamics simulations, and, thus, lack dynamic structural information. The lack
Ulf-Peter Guenther et al.
Nature, 502(7471), 385-388 (2013-09-24)
Nucleic-acid-binding proteins are generally viewed as either specific or nonspecific, depending on characteristics of their binding sites in DNA or RNA. Most studies have focused on specific proteins, which identify cognate sites by binding with highest affinities to regions with
Arto Pulk et al.
Science (New York, N.Y.), 340(6140), 1235970-1235970 (2013-07-03)
Protein synthesis by the ribosome requires the translocation of transfer RNAs and messenger RNA by one codon after each peptide bond is formed, a reaction that requires ribosomal subunit rotation and is catalyzed by the guanosine triphosphatase (GTPase) elongation factor
Xi Chen et al.
OncoTargets and therapy, 13, 4397-4409 (2020-07-02)
Recently, long non-coding RNAs (lncRNAs) have been elucidated to play essential roles in cancers, and the recognition of lncRNA expression patterns in nasopharyngeal carcinoma (NPC) may be helpful for indicating novel mechanisms underlying NPC carcinogenesis. Herein, we conducted this study
Jie Zhou et al.
Science (New York, N.Y.), 340(6140), 1236086-1236086 (2013-07-03)
Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic
Steven B Zhang et al.
Radiation research, 180(4), 407-413 (2013-09-26)
This study demonstrates that mice, similar to humans, have a common mitochondrial DNA deletion (3,860 bp) that encodes 5 transfer RNA genes and 5 polypeptide genes that is related to aging, tissue type and radiotoxicity. Our research indicates that the
Jie Zhou et al.
Science (New York, N.Y.), 345(6201), 1188-1191 (2014-09-06)
Coupled translocation of messenger RNA and transfer RNA (tRNA) through the ribosome, a process catalyzed by elongation factor EF-G, is a crucial step in protein synthesis. The crystal structure of a bacterial translocation complex describes the binding states of two
Jean Lehmann et al.
Nucleic acids research, 41(10), 5494-5502 (2013-04-13)
The structure and function of conserved motifs constituting the apex of Stem I in T-box mRNA leaders are investigated. We point out that this apex shares striking similarities with the L1 stalk (helices 76-78) of the ribosome. A sequence and
Abhishek Chatterjee et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(29), 11803-11808 (2013-07-03)
Here we report the development of a baculovirus-based delivery system that enables the efficient incorporation of unnatural amino acids into proteins in mammalian cells. We have exploited the large cargo-capacity (>30 kb) and stability of the double-stranded DNA genome of
Tamir Tuller et al.
Nucleic acids research, 43(1), 13-28 (2014-12-17)
The codon composition of the coding sequence's (ORF) 5' end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed
Tomasz W Turowski
Gene, 526(1), 23-29 (2013-05-04)
In eukaryotes, three RNA polymerases are responsible for transcription. These complex enzymes show many similarities with one another, such as several common or highly homologue subunits, while some other features, such as transcript length, diversity, processing, and transcription regulation, are
Lorenzo Peverelli et al.
Muscle & nerve, 50(2), 292-295 (2014-04-09)
A 61-year-old woman with a 5-year history of progressive muscle weakness and atrophy had a muscle biopsy characterized by a combination of dystrophic features (necrotic fibers and endomysial fibrosis) and mitochondrial alterations [ragged-red, cytochrome c oxidase (COX)-negative fibers]. Sequencing of
Manuel Neeb et al.
Journal of medicinal chemistry, 57(13), 5566-5578 (2014-06-25)
Lead optimization focuses on binding-affinity improvement. If a flat structure-activity relationship is detected, usually optimization strategies are abolished as unattractive. Nonetheless, as affinity is composed of an enthalpic and entropic contribution, factorization of both can unravel the complexity of a
Narayana Annaluru et al.
Science (New York, N.Y.), 344(6179), 55-58 (2014-03-29)
Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair
Dawid Krokowski et al.
The Journal of biological chemistry, 288(24), 17202-17213 (2013-05-07)
Endoplasmic reticulum (ER) stress-induced responses are associated with the loss of insulin-producing β-cells in type 2 diabetes mellitus. β-Cell survival during ER stress is believed to depend on decreased protein synthesis rates that are mediated via phosphorylation of the translation
Karri M Haen et al.
Gene, 535(2), 336-344 (2013-11-02)
Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate
Bo Zhang et al.
Gene, 533(1), 253-260 (2013-10-08)
To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A+T content (84.76%) and strong C skew (-0.26) was arranged in the same gene order
Min Tan et al.
Nucleic acids research, 41(10), 5513-5523 (2013-04-16)
Faithful translation of the genetic code depends on accurate coupling of amino acids with cognate transfer RNAs (tRNAs) catalyzed by aminoacyl-tRNA synthetases. The fidelity of leucyl-tRNA synthetase (LeuRS) depends mainly on proofreading at the pre- and post-transfer levels. During the
Nadezhda V Petrova et al.
Cell cycle (Georgetown, Tex.), 15(3), 337-344 (2015-12-23)
Heat stress is one of the best-studied exogenous stress factors; however little is known about its delayed effects. Recently, we have shown that heat stress induces cellular senescence-like G2 arrest exclusively in early S-phase cells. The mechanism of this arrest
Boris Slobodin et al.
Methods in molecular biology (Clifton, N.J.), 714, 387-406 (2011-03-25)
RNA metabolism involves regulatory processes, such as transcription, splicing, nuclear export, transport and localization, association with sites of RNA modification, silencing and decay, and necessitates a wide variety of diverse RNA-interacting proteins. These interactions can be direct via RNA-binding proteins
Jason C Grigg et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(18), 7240-7245 (2013-04-17)
The T box leader sequence is an RNA element that controls gene expression by binding directly to a specific tRNA and sensing its aminoacylation state. This interaction controls expression of amino acid-related genes in a negative feedback loop. The T
Crystal E Fagan et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(24), 9716-9721 (2013-05-01)
After four decades of research aimed at understanding tRNA selection on the ribosome, the mechanism by which ribosomal ambiguity (ram) mutations promote miscoding remains unclear. Here, we present two X-ray crystal structures of the Thermus thermophilus 70S ribosome containing 16S
Jonathan Somme et al.
RNA (New York, N.Y.), 20(8), 1257-1271 (2014-06-22)
The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no
Laasya Samhita et al.
Journal of bacteriology, 196(14), 2607-2615 (2014-05-13)
Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNAi) genes, encoding a special tRNA (tRNA(fMet)) required
Dan Li et al.
Gene, 545(1), 132-140 (2014-05-02)
The mayfly species Siphluriscus chinensis (Siphluriscidae) has valuable structures useful for phylogeny reconstruction, given its putative basal position within the Ephemeroptera. Here its nearly complete mitochondrial genome is sequenced. We built phylogenetic trees through multiple analytical strategies with some other
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