Search results for "Open reading frame"
showing 10 items of 167 documents
Nucleotide sequence of plasmid p4028, a cryptic plasmid from Leuconostoc oenos.
1996
Abstract TheLeuconostoc oenosplasmid p4028 was cloned in pBlueScript (SK+), and its complete nucleotide sequence was determined. The analysis of the nucleotide sequence revealed five open reading frames, all of them located on the same strand and grouped in two clusters separated by a short noncoding stretch. A similarity search against the other sequences deposited in the EMBL and GenBank databases showed that p4028 has no significant similarity with any of the sequences checked. Nevertheless, a putative ATP-binding motif was found in ORF2. A more detailed analysis of this ORF suggests that it could encode for a DNA-dependent ATPase.
Genotypic analysis at multiple loci across Kaposi's sarcoma herpesvirus (KSHV) DNA molecules: clustering patterns, novel variants and chimerism
2001
Abstract Background: the genomes of human Kaposi's sarcoma-associated herpesvirus (KSHV) display several levels of DNA sequence heterogeneity and subgrouping that show distinctive clustering patterns in related human populations. The four major subtype patterns for the hypervariable ORF-K1 protein correlate closely with the principal diasporas resulting from the migration of modern humans out of East Africa and suggest that KSHV is an ancient human virus that is transmitted primarily in a familial fashion with consequent very low recombination rates. However, chimeric genomes have also been detected, especially with regard to the presence of P versus M alleles of the ORF-K15 gene. Objective…
Characterization of a novel open reading frame, urf a, in the mitochondrial genome of fission yeast: correlation of urf a mutations with a mitochondr…
1991
Between the genes for tRNA(gin) and tRNA(ile) an open reading frame of 227 amino acids has been identified which is unique among known mitochondrial genomes and which has been termed urf a (Lang et al. 1983; Kornrumpf et al. 1984). It uses the "mitochondrial" genetic code, i.e., it contains a TGA codon, whereas all other protein-encoding genes, and all but one intronic open reading frame, use the "standard" genetic code (UGG for tryptophan). A previous paper has demonstrated that "mutator" strains show an increased formation of mitochondrial drug-resistant and respiration-deficient mutants (including deletions). In this paper we show that the mutator activity is correlated with mutations in…
Identification of Two Mannoproteins Released from Cell Walls of a Saccharomyces cerevisiae mnn1 mnn9 Double Mutant by Reducing Agents
1999
The cell wall of Saccharomyces cerevisiae represents some 30% of the total weight of the cell and is made up of β-glucans, mannose-containing glycoproteins (mannoproteins), and small amounts of chitin (9, 15). The mannoproteins can be divided into three groups according to the linkages that bind them to the structure of the cell wall: (i) noncovalently bound, (ii) covalently bound to the structural glucan, and (iii) disulfide bound to other proteins that are themselves covalently bound to the structural glucan of the cell wall (8). Our work has focused on the disulfide-bound mannoproteins, probably the least well known of the three groups mentioned above. Previous work (25) showed that trea…
Transfection analysis of expression of mRNA isoforms encoding the nuclear autoantigen La/SS-B
1997
Transcription of the gene encoding for the nuclear autoantigen La resulted in La mRNA isoforms. A promoter switching combined with an alternative splicing pathway replaced the exon 1 with the exon 1'. The exon 1' contained GC-rich regions and an oligo(U) tail of 23 uridine residues. Moreover, it encoded for three open reading frames upstream of the La protein reading frame. Despite this unusual structure, when exon 1' La mRNAs were expressed in transfected cells, both exon 1 and 1' La mRNAs were translated to La protein, whereas the upstream open reading frames of the exon 1' were not translated. In addition to full-length exon 1' La mRNAs 5'-shortened exon 1' La mRNAs were detected. The ex…
Polymorphism of mytilin B mRNA is not traslated into mature peptide
2008
Diversity of mRNAs from mytilin B, one of the five mytilins identified in the Mediterranean mussel, Mytilus galloprovincialis, has been investigated from circulating hemocytes. One mussel expressed simultaneously two to ten different mytilin B mRNAs as observed in denaturing gradient gel electrophoresis (DGGE), defining 10 individual DGGE patterns (named A to J) within the mussels from Messina, Sicily (Italy). Three patterns accounted for 79% of the individuals whereas other patterns were found in only 2-7% of the 57 analyzed mussels. Base mutations were observed at specific locations, mainly within COOH-terminus and 3'UTR, leading to 36 nucleotide sequence variants and 21 different coding …
On the origin of Metazoan adhesion receptors: cloning of integrin alpha subunit from the sponge Geodia cydonium
1997
Integrins are prominent receptors known from vertebrates and the higher phyla of invertebrates. Until now, no evidence has been provided for the existence of integrins in the lowest Metazoa, the sponges (Porifera). We have isolated and characterized a cDNA clone encoding the alpha subunit of integrin from the marine sponge Geodia cydonium (GCINTEG). The open reading frame encodes a polypeptide of 1,086 residues (118 kDa). The intracellular domain features the sequence Tyr-Phe-x-Gly-Phe-Phe-x-Arg, which is different in one residue from the characteristic consensus pattern for integrin alpha subunits. We conclude that sponges, the oldest multicellular animal phylum, already utilize the struct…
Structure and evolution of the leucine plasmids carried by the endosymbiont (Buchnera aphidicola) from aphids of the family Aphididae.
1998
In all examined species of the family Aphididae, the bacterial endosymbiont Buchnera aphidicola carries a plasmid encoding the genes leuABCD (involved in leucine biosynthesis) along with repA1, repA2 and ORF1. The gene organisation of the leucine plasmids was conserved, except in Buchnera isolated from Pterocomma populeum, where ORF1 was located in a different position. An inverted repeat (LIR1) located between repA2 and leuA is found in all of the Buchnera leucine plasmids examined. The predicted secondary structure of the LIR1 transcript conforms to a long hairpin loop, suggesting an involvement in transcription termination or messenger stability. Phylogenetic reconstruction based on repA…
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.
2012
Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of t…
Enhanced expression of a cloned and sequenced Ciona intestinalis TNFa-like (CiTNFa) gene during the LPS-induced inflammatory response.
2008
A tumor necrosis factor-alpha (TNFalpha)-like gene from Ciona intestinalis (CiTNF alpha-like) body wall challenged with bacterial lipopolysaccharide (LPS) was cloned and sequenced 4 h after LPS inoculation. An open reading frame of 936 bp encoding a propeptide of 312 amino acids (35.4 kDa) displaying a transmembrane domain from positions 7 to 29, a TACE cleavage site, and a mature peptide domain of 185 amino acids (20.9 kDa), was determined with a predicted isoelectric point of 9.4. The phylogenetic tree based on deduced amino acid sequences of invertebrate TNF-like protein and vertebrate TNFs supported the divergence between the ascidian and vertebrate TNF families, whereas D. melanogaster…