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At least 1,189 records · Page 66Linked to original sources
PubMed1989

Pause sites and regulatory role of secondary structure in RNA replication.

We analyze the correlation between pause sites and changes in enzyme boundaries within the elongation complex in template-instructed MDV-1 RNA replication. A Monte-Carlo simulation is carried out to follow the refolding events in the replica and in the portion of template strand upstream of the site where nucleotide incorporation takes place. We introduce and verify the hypothesis that the refolding events upstream of the replication fork are involved in the regulation of replication by leading to a partial relaxation of interaction between the enzyme and the growing chain. This relaxation is carried out by replacing enzyme-product binding by intra-chain pairing of the bases involved.

Base Sequence↗
PubMed2004

Noncatalytic assembly of ribonuclease III with double-stranded RNA.

Ribonuclease III (RNase III) represents a family of double-stranded RNA (dsRNA) endonucleases. The simplest bacterial enzyme contains an endonuclease domain (endoND) and a dsRNA binding domain (dsRBD). RNase III can affect RNA structure and gene expression in either of two ways: as a dsRNA-processing enzyme that cleaves dsRNA, or as a dsRNA binding protein that binds but does not cleave dsRNA. We previously determined the endoND structure of Aquifex aeolicus RNase III (Aa-RNase III) and modeled a catalytic complex of full-length Aa-RNase III with dsRNA. Here, we present the crystal structure of Aa-RNase III in complex with dsRNA, revealing a noncatalytic assembly. The major differences between the two functional forms of RNase III.dsRNA are the conformation of the protein and the orientation and location of dsRNA. The flexibility of a 7 residue linker between the endoND and dsRBD enables the transition between these two forms.

Amino Acid Sequence↗
PubMed2002

tRNA-like recognition of group I introns by a tyrosyl-tRNA synthetase.

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the catalytically active RNA structure. Previous work suggested that CYT-18 recognizes a conserved tRNA-like structure of the group I intron catalytic core. Here, directed hydroxyl-radical cleavage assays show that the nucleotide-binding fold and C-terminal domains of CYT-18 interact with the expected group I intron cognates of the aminoacyl-acceptor stem and D-anticodon arms, respectively. Further, three-dimensional graphic modeling, supported by biochemical data, shows that conserved regions of group I introns can be superimposed over interacting regions of the tRNA in a Thermus thermophilus TyrRS/tRNA(Tyr) cocrystal structure. Our results support the hypothesis that CYT-18 and other aminoacyl-tRNA synthetases interact with group I introns by recognizing conserved tRNA-like structural features of the intron RNAs.

Cloning, Molecular↗
PubMed1987

Mutations in the human adenosine deaminase gene that affect protein structure and RNA splicing.

Adenosine deaminase (ADA; adenosine aminohydrolase, EC 3.5.4.4) deficiency is one cause of the genetic disease severe combined immunodeficiency. To identify mutations responsible for ADA deficiency, we synthesized cDNAs to ADA mRNAs from two cell lines, GM2756 and GM2825A, derived from ADA-deficient immunodeficient patients. Sequence analysis of GM2756 cDNA clones revealed a different point mutation in each allele that causes amino acid changes of alanine to valine and arginine to histidine. One allele of GM2825A also has a point mutation that causes an alanine to valine substitution. The other allele of GM2825A was found to produce an mRNA in which exon 4 had been spliced out but had no other detrimental mutations. S1 nuclease mapping of GM2825A mRNAs showed equal abundance of the full-length ADA mRNA and the ADA mRNA that was missing exon 4. Several of the ADA cDNA clones extended 5' of the major initiation start site, indicating multiple start sites for ADA transcription. The point mutations in GM2756 and GM2825A and the absence of exon 4 in GM2825A appear to be directly responsible for the ADA deficiency. Comparison of a number of normal and mutant ADA cDNA sequences showed a number of changes in the third base of codons. These changes do not affect the amino acid sequence. Analyses of ADA cDNAs from different cell lines detected aberrant RNA species that either included intron 7 or excluded exon 7. Their presence is a result of aberrant splicing of pre-mRNAs and is not related to mutations that cause ADA deficiency.

Adenosine Deaminase↗
PubMed1989

Rat gene 33: analysis of its structure, messenger RNA and basal promoter activity.

Several overlapping cDNA and genomic DNA clones corresponding to mRNA g33 and gene 33, respectively, were isolated and characterized. The mRNA g33 molecule is 2971 nt in length, exclusive of a poly(A+) tail, and encodes a putative 459 amino acid protein (49,946 daltons). The 13.2 kbp gene consists of four exons, three introns, and has two initiation sites located 27 and 30 bp downstream from a TATA box. Transfection of H4IIE cells with a fusion gene 33 (-1900 to +32)/luciferase construct (pSL330A) gave rise to readily detectable luciferase activity. In addition, primer extension analysis of the gene 33/luciferase mRNA transcribed in these experiments showed that transcription initiates in the gene 33 DNA at two sites consistent with those found in vivo. Analysis of the effect of 5' deletions on basal promoter activity showed that, in relation to the promoter activity of pSL330A, approximately 40% of the activity is lost between -1643 and -1050, another approximately 40% between -550 and -475, and deletion to -55 causes a total loss of detectable luciferase activity.

Amino Acid Sequence↗
PubMed2005

Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms.

To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5' and 3' termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3' RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3' termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380-395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.

Bacteria↗
PubMed2002

In vitro selection of N peptide-binding RNA on a quartz-crystal microbalance.

We report here an in vitro selection of a hairpin loop-RNA bound to N Peptide from bacteriophage lambda on a 27 MHz quartz-crystal microbalance (QCM) to study an interaction between an RNA structure and an RNA-binding peptide. The N Peptide was immobilized on a QCM electrode and specific RNAs binding to the peptide were selected from a GNRNA pentaloop-randomized RNA library with in situ monitoring of selection processes using a QCM. After the 5th round selection, the consensus sequences including a GCGCA loop were obtained from the pentaloop library. This RNA sequence was different from a binding site of a native N Protein (boxB RNA).

Base Sequence↗
PubMed1990

Purification and molecular structure of RNA polymerase from influenza virus A/PR8.

The RNA-dependent RNA polymerase of influenza virus A/PR/8 was isolated from virus particles by stepwise centrifugation in cesium salts. First, RNP (viral RNA-NP-P proteins) complexes were isolated by glycerol gradient centrifugation of detergent-treated viruses and subsequently NP was dissociated from RNP by cesium chloride gradient centrifugation. The P-RNA (P proteins-viral RNA) complexes were further dissociated into P proteins and viral RNA by cesium trifluoroacetate (CsTFA) gradient centrifugation. The nature of P proteins was further analyzed by glycerol gradient centrifugation and immunoblotting using monospecific antibodies against each P protein. The three P proteins, PB1, PB2, and PA, sedimented altogether as fast as the marker protein with the molecular weight of about 250,000 Da. Upon addition of the template vRNA, the RNA-free P protein complex exhibited the activities of capped RNA cleavage and limited RNA synthesis. When a cell line stably expressing cDNAs for three P proteins and NP protein was examined, the three P proteins were found to be co-precipitated by antibodies against the individual P proteins. These results indicate that the influenza virus RNA-dependent RNA polymerase is a heterocomplex composed of one each of the three P proteins and that the RNA-free RNA polymerase can be isolated in an active form from virus particles. Furthermore, the three P proteins form a complex in the absence of vRNA.

Animals↗
PubMed1984

Purification and subunit structure of RNA polymerase II from different stages of Artemia development.

RNA polymerase II has been purified from different stages of Artemia development: cryptobiotic gastrulae, developing embryos and nauplii. RNA polymerase from dormant and developing embryos consists of 12 subunits of 205 000, 140 000, 32 500, 25 600, 22 000, 19 400, 18 000, 16 800, 147 000, 14 000, 12 700 and 11 500 daltons, as determined by dodecyl sulphate polyacrylamide gel electrophoresis. The enzyme from larvae contains the same polypeptides except for the higher-molecular-mass component: the larval enzyme has a subunit of 172 kDa instead of the 205-kDa subunit present in the enzyme purified from embryos. Incubation of embryonic RNA polymerase II with larval extracts results in the conversion of the 205-kDa subunit into the 172-kDa one. This conversion is inhibited by soybean trypsin inhibitor, a compound which inhibits three proteases induced during Artemia early larval development. RNA polymerase II purified from a mixture of embryos and larvae contain only the 172-kDa subunit. Our results indicate that the 172-kDa subunit present in RNA polymerase II purified from larvae is produced by proteolysis of the 205-kDa subunit during the extraction and purification of the enzyme and therefore that Artemia has only one class of RNA polymerase II.

Animals↗
PubMed1967

Fine structure of RNA codewords recognized by bacterial, amphibian, and mammalian transfer RNA.

Nucleotide sequences of 50 RNA codons recognized by amphibian and mammalian liver transfer RNA preparations were determined and compared with those recognized by Escherichia coli transfer RNA. Almost identical translations were obtained with transfer RNA from guinea pig liver, Xenopus laevis liver (South African clawed toad), and E. coli. However, guinea pig and Xenopus transfer RNA differ markedly from E. coli transfer RNA in relative response to certain trinucleotides. Transfer RNA from mammalian liver, amphibian liver, and amphibian muscle respond similarly to trinucleotide codons. Thus the genetic code is essentially universal, but transfer RNA from one organism may differ from that of another in relative response to some codons.

Amino Acid Sequence↗