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The Ras family small GTPases play a variety of essential roles in eukaryotes. Among them, classical Ras (H-Ras, K-Ras, and N-Ras) and its orthologues are conserved from yeast to human. In ascidians, which phylogenetically exist between invertebrates and vertebrates, the fibroblast growth factor (FGF)–Ras–MAP kinase signaling is required for the induction of neural system, notochord, and mesenchyme...
A bidirectional promoter can regulate the expression of two flanking genes arranged in a divergent manner. Although reports pertaining to bidirectional promoters on a genomic scale exist in mammals, little progress has been made in plants. In the present study, we performed a computational analysis of this unique class of promoters to identify overrepresented cis-regulatory motifs from three sequenced...
Arginine decarboxylase (ADC), one of the enzymes responsible for putrescine (Put) biosynthesis, has been shown to be implicated in stress response. In the current paper attempts were made to clone and characterize a gene encoding ADC from peach (Prunus persica (L.) Batsch, ‘Akatsuki’). Rapid amplification of cDNA ends (RACE) gave rise to a full-length ADC cDNA (PpADC) with a complete open reading...
Here, we constructed a phylogenetic tree of 17 bacterial phyla covering eubacteria and archaea by using a new method and 102 carefully selected orthologs from their genomes. One of the serious disturbing factors in phylogeny construction is the existence of out-paralogs that cannot easily be found out and discarded. In our method, out-paralogs are detected and removed by constructing a phylogenetic...
Methylglyoxal is mainly catabolized by two major enzymatic pathways. The first is the ubiquitous detoxification pathway, the glyoxalase pathway. In addition to the glyoxalase pathway, aldose reductase pathway also plays a crucial role in lowering the levels of methylglyoxal. The gene encoding aldose reductase (ALR) has been cloned from Leishmania donovani, a protozoan parasite causing visceral leishmaniasis...
Mutations in several steps of de novo purine synthesis lead to human inborn errors of metabolism often characterized by mental retardation, hypotonia, sensorineural hearing loss, optic atrophy, and other features. In animals, the phosphoribosylglycinamide transformylase (GART) gene encodes a trifunctional protein carrying out 3 steps of de novo purine synthesis, phosphoribosylglycinamide synthase...
Evolutionary rates of party hub and date hub proteins of Saccharomyces cerevisiae are analyzed under the perspective of ordered/disordered ness of proteins and the three dimensional structural context such as the solvent accessibility of the amino acid residues. Our results suggest that the lowering of evolutionary rate of the party hub proteins than the date hub proteins is solely contributed by...
To study evolution of dinucleotide simple sequence repeats (diSSRs) we searched recently available mammalian genomes for UTR-localized diSSRs with conserved upstream flanking sequences (CFS). There were 252 reported Homo sapiens genes containing the repeats (AC)n, (GT)n, (AG)n or (CT)n in their UTRs including 22 (8.7%) with diSSR-upstream flanking sequences conserved comparing divergent mammalian...
New genome sequence information was used to study evolution of 22 dinucleotide simple sequence repeat (diSSR) sites whose upstream flanking sequences were shown to be conserved comparing Homo sapiens with the marsupial, Monodelphis domestica. Among mammals, most of these diSSR sites were conserved both upstream and downstream of the diSSR. However, individual diSSRs were frequently replaced by alternative...
In this study, we identified and characterized a mouse brain-enriched unigene (msvop) after performing digital differential display. Msvop was the mouse ortholog of Xenopus synaptic vesicle-2-associated protein (svop), the molecular characteristics of which were unknown. The 3125-bp full-length cDNA encoded a 548-aa protein of approximately 60 kDa. A strong promoter element was found in the −200 to...
The complete mitochondrial genome sequence was determined for the human pinworm Enterobius vermicularis (Oxyurida: Nematoda) and used to infer its phylogenetic relationship to other major groups of chromadorean nematodes. The E. vermicularis genome is a 14,010-bp circular DNA molecule that encodes 36 genes (12 proteins, 22 tRNAs, and 2 rRNAs). This mtDNA genome lacks atp8, as reported for almost all...
SLC22A18, a poly-specific organic cation transporter, is paternally imprinted in humans and mice. It shows loss-of-heterozygosity in childhood and adult tumors, and gain-of-imprinting in hepatocarcinomas and breast cancers. Despite the importance of this gene, its transcriptional regulation has not been studied, and the promoter has not yet been characterized. We therefore set out to identify the...
The complete mitochondrial genome of Macaca thibetana was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequencing methods. It is 16,540 bp and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Most codon usage followed the typical pattern of vertebrates. Two rare start codons were found, in which GTG...
In all vertebrates, mature oocytes arrest at the metaphase of the II meiotic division, while some invertebrates arrest at metaphase-I, others at prophase-I. Fertilization induces completion of meiosis and entry into the first mitotic division. Several experimental models have been considered from both vertebrates and invertebrates in order to shed light on the peculiar aspects of meiotic division,...
Several transcription factors are presently known to regulate the response to cold stress. Here we describe a new positive regulator, ICE2, which is a transcription factor of the bHLH family that participates in the response to deep freezing through the cold acclimation-dependent pathway in Arabidopsis thaliana plants. An overexpression of ICE2 (as we named the At1g12860 locus) in transgenic Arabidopsis...
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