Kazuhiko Ohshima

Molecular evidence from retroposons that whales form a clade within even-toed ungulates

The origin of whales and their transition from terrestrial life to a fully aquatic existence has been studied in depth. Palaeontological,, morphological and molecular studies suggest that the order Cetacea (whales, dolphins and porpoises) is more closely related to the order Artiodactyla (even-toed ungulates, including cows, camels and pigs) than to other ungulate orders. The traditional view that the order Artiodactyla is monophyletic has been challenged by molecular analyses of variations in mitochondrial and nuclear DNA. We have characterized two families of short interspersed elements (SINEs) that were present exclusively in the genomes of whales, ruminants and hippopotamuses, but not in those of camels and pigs. We made an extensive survey of retropositional events that might have occurred during the divergence of whales and even-toed ungulates. We have characterized nine retropositional events of a SINE unit, each of which provides phylogenetic resolution of the relationships among whales, ruminants, hippopotamuses and pigs. Our data provide evidence that whales, ruminants and hippopotamuses form a monophyletic group.

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

BackgroundAbundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first comprehensive analysis of human PPs using all known human genes as queries.ResultsThe human genome was queried and 3,664 candidate PPs were identified. The most abundant were copies of genes encoding keratin 18, glyceraldehyde-3-phosphate dehydrogenase and ribosomal protein L21. A simple method was developed to estimate the level of nucleotide substitutions (and therefore the age) of PPs. A Poisson-like age distribution was obtained with a mean age close to that of the Alu repeats, the predominant human short interspersed elements. These data suggest a nearly simultaneous burst of PP and Alu formation in the genomes of ancestral primates. The peak period of amplification of these two distinct retrotransposons was estimated to be 40-50 million years ago. Concordant amplification of certain L1 subfamilies with PPs and Alus was observed.ConclusionsWe suggest that a burst of formation of PPs and Alus occurred in the genome of ancestral primates. One possible mechanism is that proteins encoded by members of particular L1 subfamilies acquired an enhanced ability to recognize cytosolic RNAs in trans.

A model for the mechanism of initial generation of short interspersed elements (SINEs)

Most animal genomes contain a large number of short interspersed elements (SINEs) that have a composite structure and contain a region that is homologous to a tRNA. The majority of SINEs have been found to be derived from a tRNALys, being categorized as members of a superfamily of tRNALys-related SINEs. The consensus sequences of five SINEs that belong to this superfamily were aligned. It was found that, in the tRNA-unrelated region, there are two sequence motifs that are almost identical among these five SINEs and are at a distance of 10–11 nucleotides from each other. This observation suggests a common evolutionary origin of these SINEs and/or some function(s) for these motifs. Similar sequences were unexpectedly found to be present in the sequences complementary to the U5 regions of several mammalian retroviruses whose primer is a tRNALys. On the basis of these findings, we propose a possible model for the generation of SINEs whereby they are derived from a “strong stop DNA” with a primer tRNA that is an intermediate in the process of reverse transcription of certain retroviruses.

Mechanisms of T-DNA transfer and integration into plant chromosomes: role of vir B , vir D4 and vir E2 and a short interspersed repetitive element (SINE) from tobacco

The present paper describes two topics on the early events during the formation of crown gall. (1) To measure an efficiency of T-DNA transfer from Agrobacterium cells to plant nuclei, we have developed a simple procedure which relies on Agrobacterium-mediated transient expression of the intron-GUS gene in plant cells. The results of experiments by this procedure indicate that products encoded by the virB locus and by the virD4 gene are necessary for transfer of T-DNA. VirE2 protein is also required for efficient transfer of T-DNA, although it is not absolutely essential. (2) We found a new family of short interspersed repetitive element (SINE) around the T-DNA integration target sites in the tobacco genome. SINEs are one of retroposons that is thought to originate from a tRNA or its gene. The SINE designated here as the TS family is the first example of a SINE family of plant bearing the significant homology to specific tRNAs including a vertebrate tRNALys which is thought to be a cognate molecule of most animal SINEs. The TS family occurs in approximately 5.0 104 copies per tobacco genome at least. Correlation between the presence of the TS family in tobacco chromosomes and integration of T-DNA will be discussed.