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Despite the wide distribution of processed pseudogenes in mammalian genomes, such as those of human and mouse, relatively little is known about their roles in genomic evolution. While gene duplications are recognized as one of the major driving forces in genome evolution, processed pseudogenes, which are retrotransposed copies of mRNAs, have been regarded as junk or selfish DNA for a long time. In...
Methionine adenosyltransferase (MAT) is an important enzyme for metabolic processes, inasmuch as its product, S-adenosylmethionine (AdoMet), plays a key role in trans-methylation, trans-sulphuration and polyamine synthesis. Our prior studies have shown that the Leishmania infantum genome contains two identical copies of the gene encoding MAT (MAT2 gene), arranged in head-to-tail configuration and...
We report the expression of endogenous CRF1 in COS-7 cells (African green monkey origin). Cloning of the coding region of CRF1 gene identified three alternatively spliced isoforms with nucleotide and predicted amino acid sequences corresponding to the membrane bound α and c and soluble e isoforms. DNA sequencing of the main isoform CRF1α showed homologies of 99%, 97% and 91% with the rhesus monkey,...
Plant UDP-glucose (UDPG) pyrophosphorylase (UGPase) is involved in the production/metabolism of UDPG, a key metabolite for sucrose and cell wall biosynthesis. Two highly similar cDNAs (UGP1 and UGP2) corresponding to UGPase were isolated from cDNA libraries of hybrid aspen (Populus tremula x tremuloides). Expression of both UGPs, as studied by DNA microarrays and EST abundance, was compared to that...
In recent decades, multiple individual genes have been studied with respect to their level of expression in liver tissue and in many cases substantial progress has been made in identifying individual factors promoting gene expression in liver. However, the overall picture is still undefined and general rules or factors regulating gene expression in liver have not yet been established. Thus, a genome-wide...
We developed a series of eight mammalian cell surface marker fusion genes by using the streptavidin gene from Streptomyces avidinii. These fusion genes are useful and non-growth-toxic selection markers for rapid-harvest transfected mammalian cells. Two streptavidin constructs were used; the longer fragment contains the native bacterial signal sequence, which the shorter fragment lacks. For expression...
To better understand Euglena gracilis gene expression under different stress conditions (Chromium, Streptomycin or darkness), we undertook a survey of the E. gracilis transcriptome by cDNA sequencing and microarray analysis. First, we constructed a non-normalized cDNA library from the E. gracilis UTEX strain and sequenced a total of 1000 cDNAs. Six hundred and ten of these ESTs were similar to either...
The 3′ untranslated regions deeply affect many properties of eukaryotic mRNA. In plants, the polyadenine control signals contained in these regions seem to be more variable than of mammals. Three cDNA libraries derived from the leaf, endosperm and stem tissues of rice were sequenced from the 3′-end. Of the 9911 transcripts analyzed, 5723 unique transcripts were identified from the leaf sequences,...
The transposition of the Ty mobile genetic element of Saccharomyces cerevisiae is induced by carcinogens. While the molecular background of spontaneous Ty1 transposition is well understood, the detailed mechanism of carcinogen induced Ty1 transposition is not clear. We found that mitochondrial functions participate in the Ty induced transposition induced by carcinogens. Contrary to the parental rho...
Ogre elements are a group of LTR retrotransposons recently discovered in legume plants, where they constitute almost 40% of the genome in some species. They are exceptional in their size (reaching 25 kb) and possess several specific features, including an intron within a polyprotein-coding region, and an extra open reading frame (ORF1) encoding a protein of unknown function located upstream of the...
Botmar1 elements are mariner-like elements (MLEs), class II transposable elements that occur in the genome of the bumble bee, Bombus terrestris. Each haploid B. terrestris genome contains about 230 Botmar1, consisting entirely of 1.3-kb and 0.85-kb elements. During their evolution in the B. terrestris genome, two Botmar1 lineages have been differentiated in terms of their nucleic acid sequences and...
Using a versatile and highly sensitive retroviral microarray, we have investigated particle preparations from three different human packaging cell lines harboring retroviral vector systems based on human immunodeficiency virus (HIV) and murine leukemia virus (MLV). 293Rev/Gag/Pol i cells inducibly express high titers of HIV-derived particles for packaging of HIV vectors. The Phoenix-GP and...
Alu elements represent a family of short interspersed DNA elements (SINEs) found in primate genomes. These are members of a group of transposable elements that integrate into the genome by the process of retrotransposition. Recent integrations of Alu elements within the human genome have generated presence/absence variants useful as DNA markers in human population studies as well as in forensic and...
The long interspersed element-1 (LINE-1 or L1) is a highly successful retrotransposon in mammals. L1 elements have continued to actively propagate subsequent to the human–chimpanzee divergence, ∼6 million years ago, resulting in species-specific inserts. Here, we report a detailed characterization of chimpanzee-specific L1 subfamily diversity and a comparison with their human-specific counterparts...
The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich...
At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low?...
It has been hypothesized that phenotypic variation in mammals could in part be due to incomplete and variable silencing of retrotransposons in somatic cells. This theory is based on the fact that some recent endogenous retroviral (ERV) insertions in the mouse exert variable effects on genes in isogenic animals, depending on the variable state of ERV methylation. In this article, we review the evidence...
Retrotransposons are ubiquitous in the plant genomes and are responsible for their plasticity. Recently, we described a novel family of gypsy-like retrotransposons, named Retand, in the dioecious plant Silene latifolia possessing evolutionary young sex chromosomes of the mammalian type (XY). Here we have analyzed long terminal repeats (LTRs) of Retand that were amplified from laser microdissected...
A large proportion of the plant LTR (Long Terminal Repeat) retrotransposons are partly or completely unable to synthesize their own machinery for transposition. However, most of these inactive or non-autonomous elements are likely able to retrotranspose, based on their insertional polymorphism. Therefore, they must be parasitic on one or more active partners. Here, we describe the parasitism of the...
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