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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
Lucía Otero et al.
RNA (New York, N.Y.), 20(7), 1023-1034 (2014-05-13)
Selenocysteine (Sec) is encoded by an UGA codon with the help of a SECIS element present in selenoprotein mRNAs. SECIS-binding protein (SBP2/SCBP-2) mediates Sec insertion, but the roles of its domains and the impact of its deficiency on Sec insertion
Robert Kopajtich et al.
American journal of human genetics, 95(6), 708-720 (2014-12-01)
Respiratory chain deficiencies exhibit a wide variety of clinical phenotypes resulting from defective mitochondrial energy production through oxidative phosphorylation. These defects can be caused by either mutations in the mtDNA or mutations in nuclear genes coding for mitochondrial proteins. The
Michael P Guy et al.
Genes & development, 28(15), 1721-1732 (2014-08-03)
Sequence variation in tRNA genes influences the structure, modification, and stability of tRNA; affects translation fidelity; impacts the activity of numerous isodecoders in metazoans; and leads to human diseases. To comprehensively define the effects of sequence variation on tRNA function
Patrick Lonergan et al.
Molecular reproduction and development, 66(3), 297-305 (2003-09-23)
In the cyclic cow, final maturation of the ovulatory follicle is initiated by the preovulatory luteinizing hormone (LH) surge. During the subsequent 24 hr period, the oocyte nucleus undergoes meiotic progression to metaphase II and several changes in cytoplasmic organization
Multilevel functional and structural defects induced by two pathogenic mitochondrial tRNA mutations.
Meng Wang et al.
The Biochemical journal, 453(3), 455-465 (2013-05-02)
Point mutations in hmtRNAs (human mitochondrial tRNAs) can cause various disorders, such as CPEO (chronic progressive external ophthalmoplegia) and MM (mitochondrial myopathy). Mitochondrial tRNALeu, especially the UUR codon isoacceptor, is recognized as a hot spot for pathogenic mtDNA point mutations.
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
Jiqiang Ling et al.
Nucleic acids research, 42(1), 499-508 (2013-09-21)
The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic
Kevin W Diebel et al.
Gene, 544(1), 8-18 (2014-04-22)
Canonical RNA polymerase III (pol III) type 2 promoters contain a single A and B box and are well documented for their role in tRNA and SINE transcription in eukaryotic cells. The genome of Murid herpesvirus 4 (MuHV-4) contains eight
Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress.
Saikia M, Jobava R, Parisien M, et al.
Molecular and Cellular Biology, 34(13), 2450-2463 (2014)
Kevin K Desai et al.
Nucleic acids research, 42(6), 3931-3942 (2014-01-18)
Archease is a 16-kDa protein that is conserved in all three domains of life. In diverse bacteria and archaea, the genes encoding Archease and the tRNA ligase RtcB are localized into an operon. Here we provide a rationale for this
Andreas M Anger et al.
Nature, 497(7447), 80-85 (2013-05-03)
Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here
Sebastian Kirchner et al.
Nature reviews. Genetics, 16(2), 98-112 (2014-12-24)
tRNAs, nexus molecules between mRNAs and proteins, have a central role in translation. Recent discoveries have revealed unprecedented complexity of tRNA biosynthesis, modification patterns, regulation and function. In this Review, we present emerging concepts regarding how tRNA abundance is dynamically
Wei Li et al.
Gene, 555(2), 169-177 (2014-12-03)
Cuora trifasciata has become one of the most critically endangered species in the world. The complete mitochondrial genome of C. trifasciata (Chinese three-striped box turtle) was determined in this study. Its mitochondrial genome is a 16,575-bp-long circular molecule that consists
Emily B Kramer et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(52), 21042-21047 (2013-12-04)
In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional--from the nucleus to the cytoplasm. It is now known that mature tRNAs also move
Mirjana Malnar et al.
Journal of cell science, 134(4) (2021-01-27)
The expanded GGGGCC repeat mutation in the C9orf72 gene is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansion is transcribed to sense and antisense RNA, which form RNA foci
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
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
Yunpeng Yang et al.
Applied and environmental microbiology, 86(13) (2020-05-03)
Small RNAs (sRNAs) are crucial regulatory molecules in organisms and are well-known not only for their roles in the control of diverse crucial biological processes but also for their value in regulation rewiring. However, to date, in Gram-positive anaerobic solventogenic
Enea Salsi et al.
Journal of molecular biology, 427(2), 454-467 (2014-12-03)
Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance
Silvia Prado et al.
Nucleic acids research, 41(12), 6190-6208 (2013-05-01)
MnmE is a homodimeric multi-domain GTPase involved in tRNA modification. This protein differs from Ras-like GTPases in its low affinity for guanine nucleotides and mechanism of activation, which occurs by a cis, nucleotide- and potassium-dependent dimerization of its G-domains. Moreover
Ewa Skowronek et al.
RNA (New York, N.Y.), 20(1), 115-130 (2013-11-20)
Mature tRNA 3' ends in the yeast Saccharomyces cerevisiae are generated by two pathways: endonucleolytic and exonucleolytic. Although two exonucleases, Rex1 and Rrp6, have been shown to be responsible for the exonucleolytic trimming, the identity of the endonuclease has been
t-RNA fragmentation as an early biomarker of (kidney) injury.
Alexander Holderied et al.
Journal of the American Society of Nephrology : JASN, 25(10), 2145-2147 (2014-05-17)
Zhongqi Zhang et al.
Biochemistry, 52(45), 8165-8176 (2013-10-17)
A mass spectrometry-based method was developed to measure amino acid substitutions directly in proteins down to a level of 0.001%. When applied to recombinant proteins expressed in Escherichia coli, monoclonal antibodies expressed in mammalian cells, and human serum albumin purified
Ling-Ling Zheng et al.
RNA (New York, N.Y.), 19(7), 863-875 (2013-05-25)
Trypanosoma brucei, a pathogen of human and domestic animals, is an early evolved parasitic protozoan with a complex life cycle. Most genes of this parasite are post-transcriptionally regulated. However, the mechanisms and the molecules involved remain largely unknown. We have
Chie Tomikawa et al.
FEBS letters, 587(21), 3575-3580 (2013-10-01)
Thermoplasma acidophilum is a thermo-acidophilic archaeon. We purified tRNA(Leu) (UAG) from T. acidophilum using a solid-phase DNA probe method and determined the RNA sequence after determining via nucleoside analysis and m(7)G-specific aniline cleavage because it has been reported that T.
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
Paul D Good et al.
Gene, 526(1), 7-15 (2013-05-28)
Transfer RNA (tRNA) genes and other RNA polymerase III transcription units are dispersed in high copy throughout nuclear genomes, and can antagonize RNA polymerase II transcription in their immediate chromosomal locus. Previous work in Saccharomyces cerevisiae found that this local
Sergei Gaidamakov et al.
Molecular and cellular biology, 34(1), 123-131 (2013-11-06)
La antigen (Sjögren's syndrome antigen B) is a phosphoprotein associated with nascent precursor tRNAs and other RNAs, and it is targeted by autoantibodies in patients with Sjögren's syndrome, systemic lupus erythematosus, and neonatal lupus. Increased levels of La are associated
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