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At least 199 records · Page 11Linked to original sources
PubMed1993

Autophosphorylation of degradation products of arginyl-tRNA synthetase protein, isolated from Bom:NMRI mouse liver.

Proteins of M(r) 140, 60, 57, 50, 22, and 14 kDa, all possessing arginyl-tRNA synthetase activity, were subjected to phosphorylation without addition of exogenous protein kinase activity. All proteins except the 14 kDa were shown to contain endogenous protein kinase activity. The product of autophosphorylation of the 60, 57, 50, and 22 kDa proteins was identified as a phosphorylated 14.9 kDa molecule. In some cases higher molecular weight phosphorylated proteins were also detected. Properties of the 60 kDa species are described.

Adenosine Triphosphate↗
PubMed1974

Effects of guanosine tetraphosphate, guanosine pentaphosphate, and beta-gamma methylenyl-guanosine pentaphosphate on gene expression of Escherichia coli in vitro.

The effects of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), both produced by E. coli, were measured on the activities of several genes in a cell-free system. Gene activity is measured as gene-directed synthesis of biochemically competent protein or transfer RNA. Both ppGpp and pppGpp stimulated the activities of the ara, lac, and trp operons and inhibited the arg operon. Production of transfer-RNA(Tyr) was unaffected by moderate levels of either ppGpp or pppGpp and only slightly inhibited at higher levels of ppGpp. Since the cell-free reaction mixtures hydrolyze pppGpp to ppGpp, we performed similar studies with a hydrolysis-resistant analog of pppGpp, the beta-gamma methylenyl derivative (pcppGpp). In general, pcppGpp shows the same inhibitory potency as pppGpp for the arg operon, but lacks the stimulatory effects on the ara, lac, and trp operons. This result suggests that the stimulation of these gene activities is specific for ppGpp.Under similar conditions, pppGpp and ppGpp show a slight inhibitory effect on the messenger-directed synthesis of beta-galactosidase and no effect on the messenger-directed synthesis of MS2 viral-coat protein. These observations, together with the fact that in the same system these nucleotides affect coupled transcription and translation, lead us to surmise that the activities of pppGpp and ppGpp are exerted at the level of RNA polymerase activity.

Acetamides↗
PubMed1973

Control of arginine biosynthesis in Escherichia coli: characterization of arginyl-transfer ribonucleic acid synthetase mutants.

The arginyl-transfer ribonucleic acid (Arg-tRNA) synthetase (EC 6.1.1.13, arginine: RNA ligase adenosine monophosphate) mutants, exhibiting nonrepressible synthesis of arginine by exogenous arginine, were employed in studies of several biochemical properties. Two of these mutants possessed Arg-tRNA synthetases with a reduced affinity for arginine, and this enzyme of another mutant had a reduced affinity for arginine-tRNA (tRNA(arg)). The mutant possessing an Arg-tRNA synthetase with an altered K(m) for tRNA(arg) was found to have reduced in vivo aminoacylation of two of the five isoaccepting species of tRNA(arg) and complete absence of aminoacylation of one of the isoaccepting species.

Acylation↗
PubMed1973

Control of arginine biosynthesis in Escherichia coli: role of arginyl-transfer ribonucleic acid synthetase in repression.

The physiological role of arginyl-transfer ribonucleic acid (Arg-tRNA) synthetase (E.C. 6.1.1.13, arginine: RNA ligase adenosine monophosphate) in repression of arginine biosynthetic enzymes was examined. Mutants with nonrepressible synthesis of arginine biosynthetic enzymes were isolated from various strains of Escherichia coli by resistance to growth inhibition by canavanine, an arginine analogue. These mutants possessed reduced Arg-tRNA synthetase activities which were qualitatively different from the synthetase activity of the wild type. The mutant enzymes exhibited turnover in vivo and were less stable in vitro than the wild type at both 4 C and 40 C; they possessed different affinities for both arginine and canavanine as measured by the three common assay systems for aminoacyl-tRNA synthetases. Furthermore, in one case it was shown that (i) the mutant possesed unaltered uptake of arginine, and (ii) that the mutant possessed diminished ability to incorporate canavanine into proteins and to attach canavanine to tRNA. These observations suggested that the mutation to canavanine resistance involved a structural change in Arg-tRNA synthetase. Likewise, the results of genetic experiments suggested that the mutants differed from the wild-type strain at only one locus, and that this lies in the region of the chromosomes that includes a structural gene for Arg-tRNA synthetase. It appears that Arg-tRNA synthetase may be involved in some way in repression by arginine of its own biosynthetic enzymes.

Amino Acyl-tRNA Synthetases↗
PubMed1976

Dual regulation by arginine of the expression of the Escherichia coli argECBH operon.

The correlation between the level of messenger ribonucleic acid (mRNA) specific for the argECBH gene cluster (argECBH mRNA) measured by ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization and the rates of synthesis of N-acetylornithine deacetylase (argE enzyme) and of argininosuccinate lyase (argH enzyme) of Escherichia coli strain K-12 were determined for steady-state growth with and without added L-arginine and during the transition periods between these two states. During the transient period after arginine removal (transient derepression), the synthesis of enzymes argE and argH was initially three to five times greater than the steady-state derepressed rate finally reached 50 min later. The level of argECHB mRNA correlated well both quantitatively and temporally with the rates of enzyme synthesis during this transition. The level of in vivo charged arginyl-transfer RNA (tRNAarg), monitored simultaneously, was initially only 5 to 10% and gradually increased to a final level of 80% after 45 min. During the transient period after arginine addition (transient repression), the rates of synthesis of enzymes argE and argH decreased to almost zero and gradually reached steady-state repressed rates after about 180 min. The argECBH mRNA level remained constant at the steady-state repressed level throughout transient repression, revealing a discontinuity between the level of this mRNA and rates of enzyme synthesis. A similar discrepancy was noted during the transition after ornithine addition. In vivo charged tRNAarg remained constant at 80% during this transition. After removal of arginine, the zero-level transient enzyme synthesis developed after only 7.5 min of arginine deprivation and was maximum after 30 min. The results suggest an accumulation of a molecule regulated by arginine that plays a role in transient repression. Our data indicate that arginyl-tRNA synthetase is not this molecule since its synthesis was unaffected by arginine. The ratios of steady-state argE and argH enzyme synthesis without arginine to that with arginine were 12 and 20, respectively, whereas the similar ratio for argECBH mRNA was 2 to 3. The repressed level of argECBH mRNA was not affected by attempts to repress or derepress the ppc+ gene (carried on the DNA used for hybridization), and the repressed level of argECBH mRNA was lowered about 50% in cells carrying an internal argBH deletion. These data taken together indicate the presence of an excess of untranslated argECBH mRNA during both transient and steady-state repression by arginine. Thus, a second regulatory mechanism, not yet defined, appears to play an important role in arginine regulation of enzyme synthesis.

Amidohydrolases↗
PubMed1983

Mitochondrial transfer RNA genes from fungi (Aspergillus nidulans) and plants (Lupinus luteus) are transcribed in Xenopus laevis oocyte nuclei.

Three plasmids containing Aspergillus nidulans mitochondrial transfer RNA genes were microinjected into the nucleus of Xenopus laevis oocytes. Plasmids that contained a single tRNACys gene or two tRNA genes (Arg and Asn) yielded tRNA-sized transcripts. Plasmids containing cloned Lupinus mitochondrial tRNA genes were also transcribed and processed in X. laevis nuclei.

Animals↗
PubMed2003

Suppression of an intrinsic strand transfer activity of HIV-1 Tat protein by its second-exon sequences.

The Tat protein of human immunodeficiency virus type 1 (HIV-1) has been shown to restrict premature reverse transcription at late stages of virus infection and to thus ensure the integrity of the viral RNA genome for packaging. To gain further insights into the roles of Tat in HIV-1 reverse transcription, we have assessed its effects on the first-strand transfer during the synthesis of minus-strand DNA through use of a reconstituted cell-free system. The results demonstrated that a form of Tat, containing only the first exon (Tat72), was able to enhance the first-strand transfer as efficiently as did the viral nucleocapsid protein. Coincidentally, this form of Tat was unable to inhibit the production of minus-strand strong-stop DNA. Further studies with various mutated forms of Tat showed that its Cys-rich region, rather than the core and Arg-rich domains, was essential for this strand transfer activity. Moreover, this activity of Tat is largely independent of the TAR RNA structure. Although full-length Tat protein (Tat86) was also able to promote strand transfer, this activity was limited by a strong overall inhibition of reverse transcription because of the presence of the second Tat exon. Other nucleic-acid-binding proteins (e.g., single-strand DNA-binding protein) were employed as negative controls and were unable to promote strand transfer in these assays. We propose that Tat possesses nucleic acid chaperone activity and can promote the first-strand transfer during HIV-1 reverse transcription; however, these activities are restricted by the second Tat exon, and the roles of these Tat activities in viral replication remain to be elucidated.

Base Sequence↗
PubMed2001

The RNA/protein symmetry hypothesis: experimental support for reverse translation of primitive proteins.

Although the "RNA-world" theory, or the RNA-first theory is renowned for a promising theory of biogenesis, it is also possible that both RNAs and proteins have coevolved forming a stable metabolic complex from the very beginning. I investigated this possibility assuming that the genetic information flowed symmetrically in the era of the origin of life, i.e. the primitive translation machinery worked in both directions (from RNA to protein and from protein to RNA). According to this RNA/protein symmetry theory, the genetic information would have come from existing cellular proteins via reverse translation. This process would have been completed in a short period of time without searching an enormous RNA sequence space. Furthermore, reverse translation would have ensured biological continuity; proteins that were essential for cellular metabolism would have been utilized in the same way as before the protein sequence information would have been transferred into the RNA sequences. I also propose a possible mechanism for the process of reverse translation. The reverse translation would proceed in the 3' to 5' direction using a set of at least 20 reverse transfer RNAs (rtRNAs) that can recognize their specific amino acid residue and carry their corresponding codon. A source of genetic information would be a primary sequence of a protein molecule. Several basic steps of reverse translation were demonstrated using rtRNA(Arg).

3' Untranslated Regions↗
PubMed1975

Primary structure of tRNA Arg II of E. coli B.

tRNA Arg II of E. coli has 77 nucleotides. There are eight minor nucleotides including inosine and 2-methyladenosine. Except for a few differences, the structure of tRNA Arg II is very similar to the structure of tRNA Arg I reported by Murao et al.3. The major difference is in the size of dihydrouridine loop. tRNA Arg II does not contain 2-thiocytosine. The unidentified nucleoside X seems to be a different modification other than nucleoside N reported to be present in tRNA Arg I.

Arginine↗
PubMed1994

Region of a conserved sequence motif in a class II tRNA synthetase needed for transfer of an activated amino acid to an RNA substrate.

The class II Escherichia coli alanine tRNA synthetase aminoacylates RNA miniduplexes, which reconstruct the acceptor end of alanine tRNA with the critical G3:U70 base pair. A benzophenone photoaffinity label attached adjacent to G3:U70 in a miniduplex substrate was previously cross-linked to a long enzyme peptide that begins at Gly161 between the class-defining motifs 2 and 3 [Musier-Forsyth, K., & Schimmel, P. (1994) Biochemistry 33, 773-779]. To identify side chains in this peptide that potentially contribute hydrogen bonding or catalytic determinants for the RNA-dependent step of the aminoacylation reaction, peptide functional side chains that are conserved among sequenced alanine enzymes (Asp, Asn, Arg, Glu, Gln, and Tyr) were individually replaced. Of the 21 mutant proteins so generated, one was identified that was not viable even though it accumulated in vivo. This Asp235-->Ala mutant enzyme is defective in the rate of transfer of the activated amino acid to the 3'-end of the RNA substrate. The conserved Asp235 is at the beginning of motif 3. By comparison with the crystal structure of the related class II yeast aspartate tRNA synthetase complexed with tRNA(Asp) (Cavarelli et al., 1993), we suggest that D235 is not in direct contact with acceptor helix base pairs such as G3:U70. Instead, we propose that D235 contributes to transfer-step interactions at the 3'-end of alanine tRNA. Because D235 in alanine tRNA synthetase is at the beginning of one of the conserved motifs that define class II tRNA synthetases, this region of the structure may in general be important for the transfer step.

Alanine-tRNA Ligase↗
PubMed2004

Arginine increases growth hormone gene expression in rat pituitary and GH3 cells.

The effect of arginine (Arg) and Ornitargin (OT) [a compound containing the aminoacids Arg, citrulline (Cit) and ornithine (Orn)] administration upon growth hormone (GH) gene expression was studied both in vivo and in vitro (hemipituitaries and GH3 cells) by Northern blot analysis. For in vivo studies, adult male Wistar rats were anesthetized, subjected to i.v. infusion of 200 microl of 150 mM NaCl (control group), Arg (15 or 150 mg) or OT (15 mg of Arg, 1 mg of Cit and 4 mg of Orn) at a rate of 20 microl/min, and killed 50 min thereafter. For the in vitro studies, hemipituitaries or GH3 cells were incubated in 1 ml of appropriate medium containing Arg (15 or 150 mg) or OT (15 mg of Arg, 1 mg of Cit and 4 mg of Orn) for 60 min. The pituitaries of the in vivo and in vitro studies and GH3 cells were subsequently processed for RNA extraction. Total RNA was subjected to electrophoresis in agarose (1%)/formaldehyde gel, transferred to a nylon membrane and subjected to hybridization with a rat GH (32)P-cDNA, and (32)P-18S rRNA probe to correct for the variability in RNA loading. After autoradiography of the membrane, the abundance of GH mRNA and 18S rRNA bands was quantified by densitometry. The in vivo study demonstrated that Arg and OT infusion induced a 2.3-fold increase in GH mRNA expression, which could result from the Arg-mediated inhibition of somatostatin release. In addition, in vitro Arg, but not OT, induced GH gene expression in hemipituitaries and GH3 cells, indicating that the aminoacid can act per se at the pituitary somatotrope level. In conclusion, our data show for the first time that arginine stimulates GH gene expression in parallel to its recognized GH-releasing activity.

Analysis of Variance↗
PubMed1985

Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides.

As part of an investigation of the tRNA genes of Mycoplasma mycoides, two HindIII fragments of mycoplasma DNA comprising 0.4 and 2.5 kilobases (kb), respectively, were cloned in pBR322 and their nucleotide sequences determined. Only one tRNA gene was found in the 0.4 kb fragment, the gene for tRNAArg with the anticodon TCT, while the 2.5 kb fragment contained nine different tRNA genes arranged in a cluster which presumably constitutes a transcriptional unit. The clustered tRNA genes, with their respective anticodons, were as follows: Arg (ACG), Pro (TGG), Ala (TGC), Met (CAT), Ile (CAT), Ser (TGA), fMet (CAT), Asp (GTC), and Phe (GAA).

Base Sequence↗
PubMed2001

Combinatorial synthesis of cholesterol ester transfer protein-mRNA ligands and screening by nondenaturating gel-electrophoresis.

RNA, as one of the biomolecules with the most structural and functional diversity, is an attractive therapeutic target.(1) Employing combinatorial chemistry methods, small peptide ligands were found, which bind to a short RNA with important biological functions. A 23-nt RNA oligonucleotide from the cholesterol ester transfer protein mRNA was chosen as a molecular target.(2) A 27-nt RNA oligonucleotide from the human immunodeficiency virus type-1 (HIV-1) TAR RNA was used to control the binding specificity.(3) Tetrapeptide libraries, composed of the amino acids Lys, Tyr, Leu, Ile, and Arg, with and without C- and N-terminal lysines, were synthesized by a combination of combinatorial and divergent solid-phase synthesis. Gel-shift affinity screening was used to extract the peptides with the best RNA binding properties. The peptide Lys-Tyr-Lys-Leu-Tyr-Lys-Cys-NH(2) (1) showing micromolar affinity to its RNA target was characterized with circular dichroism (CD), ultra violet (UV) measurement, and (1)H NMR spectroscopy.

5' Untranslated Regions↗
PubMed1986

Cloning and sequence analysis of cDNA encoding urotensin I precursor.

The primary structure of the precursor of urotensin I, a neuropeptide hormone from the caudal neurosecretory system of the carp Cyprinus carpio, has been determined by analyzing the nucleotide sequence of cloned DNA complementary to the mRNA encoding it. The precursor consists of 145 amino acid residues and the carboxyl terminus represents the 41-amino acid sequence of urotensin I, preceded by Lys-Arg and followed by Gly-Lys. Sequence homology as well as similar organization of the precursors of urotensin I and mammalian corticotropin-releasing factors suggest that they are evolutionarily related. RNA transfer blot analysis indicates that mRNA encoding the precursor of urotensin I is present only in the spinal cord and not in the brain, intestine, liver, or kidney of the carp.

Amino Acid Sequence↗
PubMed1995

Essential amino acids regulate fatty acid synthase expression through an uncharged transfer RNA-dependent mechanism.

To better understand the regulation of gene expression by amino acids, we studied the effects of these macronutrients on fatty acid synthase (FAS), an enzyme crucial for energy storage. When HepG2 cells were fed serum-free media selectively deficient in each amino acid, the omission of any single classic essential amino acid as well as Arg or His (essential in some rapidly growing cells) resulted in FAS mRNA levels that were about half of those in complete medium. Control message levels were unaffected and omission of nonessential amino acids did not alter FAS expression. FAS mRNA levels peaked 12-16 h after feeding complete and Ser (nonessential)-deficient media but did not increase in cells fed Lys (essential)-deficient medium. With Lys, FAS mRNA increased over the physiologic concentration range of 15-150 microM, and low concentrations of lysine decreased FAS but not apoB protein mass. Transcription inhibitors mimicked treatment with Lys-deficient media, and nuclear run-off assays showed that Lys-deficient media abolished FAS but not apoB transcription. After treatment with Lys-deficient media, the intracellular Lys pool was rapidly depleted in association with an increase of uncharged (deacylated) tRNA Lys from < 1 to 64% of available tRNA Lys. Even in the presence of the essential amino acid His, increasing the level of uncharged tRNA His with histidinol, a competitive inhibitor of the histidinyl-tRNA synthetase, blocked FAS expression. Tyrosinol treatment did not alter FAS mRNA levels. These results suggest that essential amino acids regulate FAS expression by altering uncharged tRNA levels, a novel mechanism for nutrient control of gene expression in mammalian cells.

Amino Acids, Essential↗