scholarly journals The RNA origin of transfer RNA aminoacylation and beyond

2011 ◽  
Vol 366 (1580) ◽  
pp. 2959-2964 ◽  
Author(s):  
Hiroaki Suga ◽  
Gosuke Hayashi ◽  
Naohiro Terasaka
Keyword(s):  
Amino Acids ◽  
Evolutionary History ◽  
Transfer Rna ◽  
Translation System ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Rna Catalysts ◽  
Modern System ◽  
History Of

Aminoacylation of tRNA is an essential event in the translation system. Although in the modern system protein enzymes play the sole role in tRNA aminoacylation, in the primitive translation system RNA molecules could have catalysed aminoacylation onto tRNA or tRNA-like molecules. Even though such RNA enzymes so far are not identified from known organisms, in vitro selection has generated such RNA catalysts from a pool of random RNA sequences. Among them, a set of RNA sequences, referred to as flexizymes (Fxs), discovered in our laboratory are able to charge amino acids onto tRNAs. Significantly, Fxs allow us to charge a wide variety of amino acids, including those that are non-proteinogenic, onto tRNAs bearing any desired anticodons, and thus enable us to reprogramme the genetic code at our will. This article summarizes the evolutionary history of Fxs and also the most recent advances in manipulating a translation system by integration with Fxs.

scholarly journals Chemical aminoacylation of tRNAs with fluorinated amino acids for in vitro protein mutagenesis

2010 ◽  
Vol 6 ◽  
Author(s):  
Shijie Ye ◽  
Allison Ann Berger ◽  
Dominique Petzold ◽  
Oliver Reimann ◽  
Benjamin Matt ◽  
...  
Keyword(s):  
Amino Acids ◽  
Translation System ◽  
Biologically Relevant ◽  
Fluorinated Amino Acids ◽  
Free Translation ◽  
Trna Species ◽  
A Cell ◽  
Protein Environment ◽  
Vitro Protein

This article describes the chemical aminoacylation of the yeast phenylalanine suppressor tRNA with a series of amino acids bearing fluorinated side chains via the hybrid dinucleotide pdCpA and ligation to the corresponding truncated tRNA species. Aminoacyl-tRNAs can be used to synthesize biologically relevant proteins which contain fluorinated amino acids at specific sites by means of a cell-free translation system. Such engineered proteins are expected to contribute to our understanding of discrete fluorines’ interaction with canonical amino acids in a native protein environment and to enable the design of fluorinated proteins with arbitrary desired properties.

scholarly journals Identification of a talin binding site in the cytoskeletal protein vinculin.

1989 ◽  
Vol 109 (6) ◽  
pp. 2917-2927 ◽  
Author(s):  
P Jones ◽  
P Jackson ◽  
G J Price ◽  
B Patel ◽  
V Ohanion ◽  
...  
Keyword(s):  
Amino Acids ◽  
In Vitro Transcription ◽  
Binding Activity ◽  
Cytoskeletal Protein ◽  
Translation System ◽  
Cos Cells ◽  
Cell Matrix ◽  
Do So

Binding of the cytoskeletal protein vinculin to talin is one of a number of interactions involved in linking F-actin to cell-matrix junctions. To identify the talin binding domain in vinculin, we expressed the NH2-terminal region of the molecule encoded by two closely similar, but distinct vinculin cDNAs, using an in vitro transcription translation system. The 5' Eco RI-Bam HI fragment of a partial 2.89-kb vinculin cDNA encodes a 45-kD polypeptide containing the first 398 amino acids of the molecule. The equivalent restriction enzyme fragment of a second vinculin cDNA (cVin5) lacks nucleotides 746-867, and encodes a 41-kD polypeptide missing amino acids 167-207. The radiolabeled 45-kD vinculin polypeptide bound to microtiter wells coated with talin, but not BSA, and binding was inhibited by unlabeled vinculin. In contrast, the 41-kD vinculin polypeptide was devoid of talin binding activity. The role of residues 167-207 in talin binding was further analyzed by making a series of deletions spanning this region, each deletion of seven amino acids contiguous with the next. Loss of residues 167-173, 174-180, 181-187, 188-194, or 195-201 resulted in a marked reduction in talin binding activity, although loss of residues 202-208 had much less effect. When the 45-kD vinculin polypeptide was expressed in Cos cells, it localized to cell matrix junctions, whereas the 41-kD polypeptide, lacking residues 167-207, was unable to do so. Interestingly, some deletion mutants with reduced ability to bind talin in vitro, were still able to localize to cell matrix junctions.

VERIFICATION OF PHYLOGENETIC INFERENCE PROGRAMS USING METAMORPHIC TESTING

2011 ◽  
Vol 09 (06) ◽  
pp. 729-747 ◽  
Author(s):  
MD. SHAIK SADI ◽  
FEI-CHING KUO ◽  
JOSHUA W. K. HO ◽  
MICHAEL A. CHARLESTON ◽  
T. Y. CHEN
Keyword(s):  
Amino Acids ◽  
Software Testing ◽  
Evolutionary History ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Testing Technique ◽  
Metamorphic Testing ◽  
History Of ◽  
Scoring Algorithms

Many phylogenetic inference programs are available to infer evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids. These programs are often used to infer the evolutionary history of species. However, in most cases it is impossible to systematically verify the correctness of the tree returned by these programs, as the correct evolutionary history is generally unknown and unknowable. In addition, it is nearly impossible to verify whether any non-trivial tree is correct in accordance to the specification of the often complicated search and scoring algorithms. This difficulty is known as the oracle problem of software testing: there is no oracle that we can use to verify the correctness of the returned tree. This makes it very challenging to test the correctness of any phylogenetic inference programs. Here, we demonstrate how to apply a simple software testing technique, called Metamorphic Testing, to alleviate the oracle problem in testing phylogenetic inference programs. We have used both real and randomly generated test inputs to evaluate the effectiveness of metamorphic testing, and found that metamorphic testing can detect failures effectively in faulty phylogenetic inference programs with both types of test inputs.

scholarly journals An RNA polymerase ribozyme that synthesizes its own ancestor

2020 ◽  
Vol 117 (6) ◽  
pp. 2906-2913 ◽  
Author(s):  
Katrina F. Tjhung ◽  
Maxim N. Shokhirev ◽  
David P. Horning ◽  
Gerald F. Joyce
Keyword(s):  
Rna Polymerase ◽  
High Efficiency ◽  
Class I ◽  
Catalytic Core ◽  
Rna Molecules ◽  
Evolving System ◽  
History Of ◽  
Successive Generations ◽  
Life On Earth

The RNA-based organisms from which modern life is thought to have descended would have depended on an RNA polymerase ribozyme to copy functional RNA molecules, including copying the polymerase itself. Such a polymerase must have been capable of copying structured RNAs with high efficiency and high fidelity to maintain genetic information across successive generations. Here the class I RNA polymerase ribozyme was evolved in vitro for the ability to synthesize functional ribozymes, resulting in the markedly improved ability to synthesize complex RNAs using nucleoside 5′-triphosphate (NTP) substrates. The polymerase is descended from the class I ligase, which contains the same catalytic core as the polymerase. The class I ligase can be synthesized by the improved polymerase as three separate RNA strands that assemble to form a functional ligase. The polymerase also can synthesize the complement of each of these three strands. Despite this remarkable level of activity, only a very small fraction of the assembled ligases retain catalytic activity due to the presence of disabling mutations. Thus, the fidelity of RNA polymerization should be considered a major impediment to the construction of a self-sustained, RNA-based evolving system. The propagation of heritable information requires both efficient and accurate synthesis of genetic molecules, a requirement relevant to both laboratory systems and the early history of life on Earth.

scholarly journals Autoantibodies reactive to adrenocorticotropic hormone can alter cortisol secretion in both aggressive and nonaggressive humans

2018 ◽  
Vol 115 (28) ◽  
pp. E6576-E6584 ◽  
Author(s):  
Henning Værøy ◽  
Csaba Adori ◽  
Romain Legrand ◽  
Nicolas Lucas ◽  
Jonathan Breton ◽  
...  
Keyword(s):  
Amino Acids ◽  
Adrenocorticotropic Hormone ◽  
Cortisol Secretion ◽  
Adrenal Cells ◽  
Igg Binding ◽  
History Of ◽  
Response To Stress ◽  
Underlying Mechanisms ◽  
Epitope Binding

Violent aggression in humans may involve a modified response to stress, but the underlying mechanisms are not well understood. Here we show that naturally present autoantibodies reactive to adrenocorticotropic hormone (ACTH) exhibit distinct epitope-binding profiles to ACTH peptide in subjects with a history of violent aggression compared with controls. Namely, while nonaggressive male controls displayed a preferential IgG binding to the ACTH central part (amino acids 11–24), subjects who had committed violent acts of aggression had IgG with increased affinity to ACTH, preferentially binding to its N terminus (amino acids 1–13). Purified IgGs from approximately half of the examined sera were able to block ACTH-induced cortisol secretion of human adrenal cells in vitro, irrespective of the source of sample (from a control subject or a violent aggressor). Nevertheless, in the resident–intruder test in mice, i.p. injection of residents with ACTH and IgG from aggressive subjects, but not from control subjects, shortened latency for the first attack against intruders. Immunohistochemical screening of violent aggressors’ sera on rat brain and pituitary sections did not show IgG binding to ACTH-producing cells, but 4 of 16 sera revealed selective binding to a nonidentified antigen in vasopressinergic neurons of the hypothalamic paraventricular and supraoptic nuclei. Thus, the data show that ACTH-reactive plasmatic IgGs exhibit differential epitope preference in control and violently aggressive subjects. These IgGs can modulate ACTH-induced cortisol secretion and, hence, are involved in the regulation of the stress response. However, the possible role of ACTH-reactive autoantibodies in aggressive behavior needs further investigation.

scholarly journals Effect of lipids, in particular cholesteryl 14-methylhexadecanoate, on the incorporation of labelled amino acids into transfer ribonucleic acid in vitro

1968 ◽  
Vol 110 (1) ◽  
pp. 1-8 ◽  
Author(s):  
J. Hradec ◽  
Z. Dušek
Keyword(s):  
Amino Acids ◽  
Ribosomal Protein ◽  
Free Cholesterol ◽  
Protein Hydrolysate ◽  
Transfer Rna ◽  
Enzymic Activity ◽  
Cholesteryl Esters ◽  
Energy Dependent ◽  
Rna Complexes

1. Rat liver pH5 enzymes and cell sap extracted with various organic solvents showed a variable decreased incorporation of labelled amino acids into s-RNA (‘soluble’ or transfer RNA) in vitro. 2. The original enzymic activity could be fully restored, though at different rates, by the addition of lipid extracts in quantities corresponding to those originally present. 3. Of the main lipid groups separated from the extract, only free cholesterol and cholesteryl esters were able to reactivate the extracted pH5 enzymes in the same way as the whole lipid extract. 4. Addition of pure cholesteryl 14-methylhexadecanoate also fully restored the enzymic activity. 5. There was no energy-dependent incorporation of labelled amino acids into ribosomal protein in the presence of extracted cell sap. Addition of cholesteryl 14-methylhexadecanoate fully restored the activity of the cell sap to incorporate labelled leucine and lysine into ribosomal protein and enhanced the incorporation of labelled protein hydrolysate and phenylalanine over the level found with the corresponding non-extracted preparations. 6. It is concluded that lipids play an important role in the synthesis of aminoacyl-s-RNA complexes and that cholesteryl 14-methylhexadecanoate may be the active lipid in this respect.

scholarly journals EXPRESSION AND FUNCTIONAL INTERACTION OF CHICKEN RbAp46 POLYPEPTIDE WITH HISTONES, HISTONE DEACETYLASE-1, AND HISTONE ACETYLTRANSFERASE-1

2013 ◽  
Vol 13 (2) ◽  
pp. 136-141
Author(s):  
Ahyar Ahmad ◽  
Harningsih Karim
Keyword(s):  
Amino Acids ◽  
Histone Acetyltransferase ◽  
Single Step ◽  
In Vitro Translation ◽  
Translation System ◽  
Functional Interaction ◽  
In Vitro Experiment ◽  
Histone Deacetylase 1 ◽  
Agarose Beads

In this study, we cloned and sequenced cDNA encoding the chicken p46 polypeptide, RbAp46. The cDNA encoding a protein consists of 424 amino acids is a member of the WD protein family, with seven WD repeat motifs, and exhibits 90.3% identity to RbAp48, and 94.3% identity to the human RbAp46. The RbAp46 fusion protein were synthesized by in vitro translation system and in Escherichia coli under induction by 50 µM IPTG and single step purified with glutathione-Agarose beads, showed that GST-tagged protein of approximately 72 kDa. The in vitro experiment established that RbAp46 interacts with chicken histones, chHDAC-1, and chHAT-1. The in vitro immunoprecipitation experiment, involving truncated mutants of RbAp46, revealed not only that two regions comprising amino acids 33-179 and 375-404 are necessary for its binding to H2B, but also that two regions comprising amino acids 1-32 and 405-424 are necessary for its binding to H4. Furthermore, the GST pulldown affinity assay, involving truncated mutants of RbAp46, revealed that a region comprising amino acids 359-404 binds to chHAT-1 in vitro. Taken together, these results indicate not only that RbAp46 should participate differentially in a number of DNA-utilizing processes through interactions of its distinct regions with histones and chHAT-1, but also that the proper propeller structure of RbAp46 is not necessary for its interaction with chHAT-1.

scholarly journals Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites

2020 ◽  
Author(s):  
Alexander P. Gultyaev ◽  
Monique I. Spronken ◽  
Mathis Funk ◽  
Ron A.M. Fouchier ◽  
Mathilde Richard
Keyword(s):  
Amino Acids ◽  
Cleavage Site ◽  
Influenza A ◽  
Rna Recombination ◽  
Influenza A Viruses ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Basic Amino Acids ◽  
Molecular Determinant ◽  
Ha Protein

ABSTRACTThe presence of multiple basic amino acids in the protease cleavage site of the hemagglutinin (HA) protein is the main molecular determinant of virulence of highly pathogenic avian influenza (HPAI) viruses. Recombination of HA RNA with other RNA molecules of host or virus origin is a dominant mechanism of multi basic cleavage site (MBCS) acquisition for H7 subtype HA. Using alignments of HA RNA sequences from documented cases of MBCS insertion due to recombination, we show that such recombination with host RNAs is most likely to occur at particular hotspots in ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and viral RNAs. The locations of these hotspots in highly abundant RNAs indicate that RNA recombination is facilitated by the binding of small nucleolar RNA (snoRNA) near the recombination points.

scholarly journals Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage

2021 ◽  
Author(s):  
Sydni Caet Smith ◽  
Jennifer Gribble ◽  
Julia R. Diller ◽  
Michelle A. Wiebe ◽  
Timothy W. Thoner ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Rna Virus ◽  
Serial Passage ◽  
Viral Population ◽  
Rna Recombination ◽  
Chronic Infections ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Mammalian Orthoreovirus

For viruses with segmented genomes, genetic diversity is generated by genetic drift, reassortment, and recombination. Recombination produces RNA populations distinct from full-length gene segments and can influence viral population dynamics, persistence, and host immune responses. Viruses in the Reoviridae family, including rotavirus and mammalian orthoreovirus (reovirus), have been reported to package segments containing rearrangements or internal deletions. Rotaviruses with RNA segments containing rearrangements have been isolated from immunocompromised and immunocompetent children and in vitro following serial passage at relatively high multiplicity. Reoviruses that package small, defective RNA segments have established chronic infections in cells and in mice. However, the mechanism and extent of Reoviridae RNA recombination are undefined. Towards filling this gap in knowledge, we determined the titers and RNA segment profiles for reovirus and rotavirus following serial passage in cultured cells. The viruses exhibited occasional titer reductions characteristic of interference. Reovirus strains frequently accumulated segments that retained 5′ and 3′ terminal sequences and featured large internal deletions, while similarly fragmented segments were rarely detected in rotavirus populations. Using next-generation RNA-sequencing to analyze RNA molecules packaged in purified reovirus particles, we identified distinct recombination sites within individual viral genome segments. Recombination junctions were frequently but not always characterized by short direct sequence repeats upstream and downstream that spanned junction sites. Taken together, these findings suggest that reovirus accumulates defective gene segments featuring internal deletions during passage and undergoes sequence-directed recombination at distinct sites. IMPORTANCE Viruses in the Reoviridae family include important pathogens of humans and other animals and have segmented RNA genomes. Recombination in RNA virus populations can facilitate novel host exploration and increased disease severity. The extent, patterns, and mechanisms of Reoviridae recombination and the functions and effects of recombined RNA products are poorly understood. Here, we provide evidence that mammalian orthoreovirus regularly synthesizes RNA recombination products that retain terminal sequences but contain internal deletions, while rotavirus rarely synthesizes such products. Recombination occurs more frequently at specific sites in the mammalian orthoreovirus genome, and short regions of identical sequence are often detected at junction sites. These findings suggest that mammalian orthoreovirus recombination events are directed in part by RNA sequences. An improved understanding of recombined viral RNA synthesis may enhance our capacity to engineer improved vaccines and virotherapies in the future.

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