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The mechanism by which modified single-stranded oligonucleotides (MSSOs) direct base changes in genes is not completely understood, but there is evidence that DNA damage, repair and cell cycle checkpoint proteins are involved in the targeted nucleotide exchange (TNE) process. We are interested in the role of the mismatch repair protein, Msh2 in the correction of a frameshift mutation in both yeast...
The xenobiotic-activated nuclear receptors PXR (pregnane X receptor) and CAR (constitutive androstane receptor) and the vitamin D 3 -activated nuclear receptor VDR regulate steroid and xenobiotic metabolism by inducing the phase I cytochrome P450 monooxygenases, phase II conjugating transferases, and the phase III transporters, which mediate the efflux of water-soluble lipid metabolites from...
cDNA libraries were constructed from the following developmental stages (tissues) of the Atlantic halibut (Hippoglossus hippoglossus): 2-cell stage (embryos), 1 day-old yolk sac larvae (trunk) and juvenile (fast skeletal muscle). A total of 4249 high quality expressed sequence tags from the three libraries were clustered into a partial transcriptome of 2124 putative genes. A large proportion of the...
We and others previously showed that, in some lines of prion protein (PrP)-knockout mice, the downstream PrP-like protein (PrPLP/Dpl) was abnormally expressed in brains partly due to impaired cleavage/polyadenylation of the residual PrP promoter-driven pre-mRNA despite the presence of a poly(A) signal. In this study, we newly established an in vitro transient transfection system in which abnormal...
Disposal of misfolded proteins from the lumen of the endoplasmic reticulum (ER) is one of the quality control mechanisms present in the protein secretory pathway. Through ER-associated degradation, misfolded substrates are targeted to the cytosol where they are degraded by proteasomes. Here we describe the identification of a human ER-associated 43-kD protein (ERp43) by sequencing of the subtraction...
Patterns of nucleotide substitution at orthologous loci were examined between three genomes of Ehrlichia ruminantium, the causative agent of heartwater disease of ruminants. The most recent common ancestor of two genomes (Erwe and Erwo) belonging to the Welgevonden strain was estimated to have occurred 26,500–57,000 years ago, while the most recent common ancestor of these two genomes and the Erga...
We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher...
RecX is a regulator of RecA activity by interacting with RecA protein or RecA filaments. Genes encoding RecX were found in genomes of a wide diversity of bacteria and some plants (e.g., Arabidopsis thaliana and Oryza sativa). Our comparative genome analysis showed that although members of the RecX family are found in many bacterial species, they are not found in archaea and the only gene found in...
Mammalian HMGB proteins are abundant chromatin components, and are characterized by the presence of 2 HMG-box domains and an acidic tail. HMG boxes are present in a large number of DNA-binding proteins, and HMGB chromatin proteins represent a small and specific subset of HMG-box proteins. The comparison of DNA sequences that code for HMG-box proteins suggests that the ancestral HMG box was coded by...
The synthesis of the protein antizyme requires a +1 ribosomal frameshift event. The frameshifting serves as a regulatory sensor. Antizyme homologs have been identified in diverse organisms ranging from yeast to human and characterized in a disparate subset. Most vertebrates have multiple antizyme paralogs. Here we present identification in the zebrafish Danio rerio of a heretofore unknown member of...
We report here the molecular characterization of the basic repeating unit of a novel repetitive family, partially inverted repeat (PIR), previously identified from chicken genome. This repetitive DNA family shares a close evolutionary relationship with XhoI/EcoRI repeats and chicken nuclear-membrane-associated (CNM) repeat. Sequence analyses reveal the 1430 bp basic repeating unit can be divided into...
Alternative splicing is an important mechanism to generate proteome diversity in higher eukaryotic organisms. We searched for splice variants of the human Adhesion family of G protein-coupled receptors (GPCRs) using mRNA sequences and expressed sequence tags. The results presented here describe 53 human splice variants among the 33 Adhesion GPCRs. Many of these variants appear to be coding for “functional”...
Apparent full-length cDNA sequences coding for manganese superoxide dismutase (HvMnSOD) and extracellular superoxide dismutase (HvEC-SOD) were isolated from Hydra vulgaris in order to understand their expression and 3D structures; and explore their possibility of being used as for biomarkers for environmental stress and toxicity. The deduced HvMnSOD protein consists of 219 amino acids of which first...
The homeobox genes comprise a large gene superfamily characterised by a conserved DNA motif encoding the homeodomain. Most homeodomain proteins function as transcription factors, and many have important roles in embryonic development and cell differentiation. Here we describe, annotate and name four novel homeobox genes in the human genome: ARGFX, DPRX, TPRX1 and DUXA. Each has generated multiple...
Based on bioinformatics analysis, we previously hypothesized the existence of a bipartite TDPOZ protein family members of which carry the TRAF domain (TD) and POZ/BTB [Huang, C.-J., Chen, C.-Y., Chen, H.-H., Tsai, S.-F., Choo, K.-B., 2004. TDPOZ, a family of bipartite animal and plant proteins that contain the TRAF (TD) and POZ/BTB domains. Gene 324, 117–127.]. Conservation in animals and plants suggests...
Using functional genomic and protein structural data we studied the effects of protein complexity (here defined as the number of subunit types in a protein) on gene dispensability and gene duplicability. We found that in terms of gene duplicability the major distinction in protein complexity is between hetero-complexes, each of which includes at least two different types of subunits (polypeptides),...
Hox cluster has key roles in regulating the patterning of the antero-posterior axis in a metazoan embryo. It consists of the anterior, central and posterior genes; the central genes have been identified only in bilaterians, but not in cnidarians, and are responsible for archiving morphological complexity in bilaterian development. However, their evolutionary history has not been revealed, that is,...
Cytochromes P450 (CYPs) comprise a superfamily of enzymes involved in various physiological functions, including the metabolism of drugs and carcinogenic compounds present in food, making them of great importance for human health. The possibility that CYPs could be broadening or changing substrate specificity in accordance to the high diversity of xenobiotics compounds environmentally available suggests...
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