Biomedical subjects

Akira Kawabe

Publications and source records attributed to Akira Kawabe.

At least 19 recordsLinked to original sources

PubMed2007

Characterization of a splicing variant of plant Aurora kinase.

Aurora kinases play a key role in chromosome segregation and cytokinesis. In plants, three Aurora kinases (AtAUR1-AtAUR3) have been identified in Arabidopsis thaliana. Here, we report an AtAUR2 splicing variant (AtAUR2S), which lacks the fourth exon encoding a part of the kinase domain of AtAUR2. AtAUR2S was shown to have lost its kinase activity to phosphorylate histone H3 at Ser10; however, it maintained its ability to bind to histone H3. The localization pattern of AtAUR2S was the same as that of AtAUR2. The findings suggest that AtAUR2S affects cell division by competing with AtAUR2.

Amino Acid Sequence↗

PubMed2006

Patterns of DNA variation among three centromere satellite families in Arabidopsis halleri and A. lyrata.

We describe patterns of DNA variation among the three centromeric satellite families in Arabidopsis halleri and lyrata. The newly studied subspecies (A. halleri ssp. halleri and A. lyrata ssp. lyrata and petraea), like the previously studied A. halleri ssp. gemmifera and A. lyrata ssp. kawasakiana, have three different centromeric satellite families, the older pAa family (also present in A. arenosa) and two families, pAge1 and pAge2, that probably evolved more recently. Sequence variability is high in all three satellite families, and the pAa sequences do not cluster by their species of origin. Diversity in the pAge2 family is complex, and different from variation among copies of the other two families, showing clear evidence for exchange events among family members, especially in A. halleri ssp. halleri. In A. lyrata ssp. lyrata there is some evidence for recent rapid spread of pAge2 variants, suggesting selection favoring these sequences.

Arabidopsis↗

PubMed2006

Duplication of centromeric histone H3 (HTR12) gene in Arabidopsis halleri and A. lyrata, plant species with multiple centromeric satellite sequences.

Arabidopsis halleri and lyrata have three different major centromeric satellite sequences, a unique finding for a diploid Arabidopsis species. Since centromeric histones coevolve with centromeric satellites, these proteins would be predicted to show signs of selection when new centromere satellites have recently arisen. We isolated centromeric protein genes from A. halleri and lyrata and found that one of them, HTR12 (CENP-A), is duplicated, while CENP-C is not. Phylogenetic analysis indicates that the HTR12 duplication occurred after these species diverged from A. thaliana. Genetic mapping shows that HTR12 copy B has the same genomic location as the A. thaliana gene; the other copy (A, at the other end of the same chromosome) is probably the new copy. To test for selection since the duplication, we surveyed diversity at both HTR12 loci within A. lyrata. Overall, there is no strong evidence for an "evolutionary arms race" causing multiple replacement substitutions. The A. lyrata HTR12B sequences fall into three classes of haplotypes, apparently maintained for a long time, but they all encode the same amino acid sequence. In contrast, HTR12A has low diversity, but many variants are amino acid replacements, possibly due to independent selective sweeps within populations of the species.

Arabidopsis↗

PubMed2006

Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata.

We investigated DNA sequence diversity for loci on chromosomes 1 and 2 in six natural populations of Arabidopsis lyrata and tested for the role of natural selection in structuring genomewide patterns of variability, specifically examining the effects of recombination rate on levels of silent polymorphism. In contrast with theoretical predictions from models of genetic hitchhiking, maximum-likelihood-based analyses of diversity and divergence do not suggest reduction of diversity in the region of suppressed recombination near the centromere of chromosome 1, except in a single population from Russia, in which the pericentromeric region may have undergone a local selective sweep or demographic process that reduced variability. We discuss various possibilities that might explain why nucleotide diversity in most A. lyrata populations is not related to recombination rate, including genic recombination hotspots, and low gene density in the low recombination rate region.

Arabidopsis↗

PubMed2006

Centromere locations and associated chromosome rearrangements in Arabidopsis lyrata and A. thaliana.

We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping.

Arabidopsis↗

PubMed2006

Polymorphic chromosomal specificity of centromere satellite families in Arabidopsis halleri ssp. gemmifera.

The chromosomal localizations of repetitive DNA clusters (ribosomal DNA and centromere satellites) were analyzed by fluorescent in situ hybridization in five strains of Arabidopsis halleri ssp. gemmifera. All five A. gemmifera strains have three chromosome pairs with 45S (5.8S-16S-26S) rDNA loci, and one pair with both 5S and 45S rDNA loci. These localizations are different from that of A. thaliana. Very unusually, there are three families of centromeric satellite DNAs (pAa, pAge1, and pAge2), and they showed polymorphism among the five strains studied. Overall, we found four different centromere satellite compositions. A plant from Fumuro was heterozygous for the chromosome specificities of centromere satellite families, possibly due to a reciprocal translocation involving centromere regions. Changes of centromeric satellite repeats appear to be rapid and frequent events in the history of A. gemmifera, and seem to occur by exchanging clusters as units.

Arabidopsis↗

PubMed2006

Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location.

To add detail to the genetic map of Arabidopsis lyrata, and compare it with that of A. thaliana, we have developed many additional markers in the A. lyrata linkage groups, LG1 and LG2, corresponding to A. thaliana chromosome 1. We used a newly developed method for marker development for single nucleotide polymorphisms present in gene sequences, plus length differences, to map genes in an A. lyrata family, including variants in several genes close to the A. thaliana centromere 1, providing the first data on the location of an A. lyrata centromere; we discuss the implications for the evolution of chromosome 1 of A. thaliana. With our larger marker density, large rearrangements between the two Arabidopsis species are excluded, except for a large inversion on LG2. This was previously known in Capsella; its presence in A. lyrata suggests that, like most other rearrangements, it probably arose in the A. thaliana lineage. Knowing that marker orders are similar, we can now compare homologous, non-rearranged map distances to test the prediction of more frequent crossing-over in the more inbreeding species. Our results support the previous conclusion of similar distances in the two species for A. lyrata LG1 markers. For LG2 markers, the distances were consistently, but non-significantly, larger in A. lyrata. Given the two species' large DNA content difference, the similarity of map lengths, particularly for LG1, suggests that crossing-over is more frequent across comparable physical distances in the inbreeder, A. thaliana, as predicted.

Arabidopsis↗

PubMed2006

Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates.

We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1.23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size.

Arabidopsis↗

PubMed2006

Aurora kinase is required for chromosome segregation in tobacco BY-2 cells.

Post-translational modifications of core histone tails play crucial roles in chromatin structure and function. Although phosphorylation of Ser10 and Ser28 (H3S10ph and H3S28ph) of histone H3 is ubiquitous among eukaryotes, the phosphorylation mechanism during the cell cycle remains unclear. In the present study, H3S10ph and H3S28ph in tobacco BY-2 cells were observed in the pericentromeric regions during mitosis. Moreover, the Aurora kinase inhibitor Hesperadin inhibited the kinase activity of Arabidopsis thaliana Aurora kinase 3 (AtAUR3) in phosphorylating both Ser10 and Ser28 of histone H3 in vitro. Consistently, Hesperadin inhibited both H3S10ph and H3S28ph during mitosis in BY-2 cells. These results indicate that plant Aurora kinases phosphorylate not only Ser10, but also Ser28 of histone H3 in vivo. Hesperadin treatment increased the ratio of metaphase cells, while the ratio of anaphase/telophase cells decreased, although the mitotic index was not affected in Hesperadin-treated cells. These results suggest that Hesperadin induces delayed transition from metaphase to anaphase, and early exit from mitosis after chromosome segregation. In addition, micronuclei were observed frequently and lagging chromosomes, caused by the delay and failure of sister chromatid separation, were observed at anaphase and telophase in Hesperadin-treated BY-2 cells. The data obtained here suggest that plant Aurora kinases and H3S10ph/H3S28ph may have a role in chromosome segregation and metaphase/anaphase transition.

Arabidopsis Proteins↗

PubMed2006

Chromosome-specific satellite sequences in Turritis glabra.

Two novel repetitive sequence families were isolated from Turritis glabra (2n = 2x = 12). These two repeat families are similar to those of centromeric repeats in Arabidopsis thaliana, are co-localized on one chromosome pair, and differ by about 20% from each other. Phylogenetic analysis revealed that the two repeat families of T. glabra are more similar to each other than to the centromeric repeat families of other Arabidopsis and related species. The relationships of satellite sequences reflected the species phylogeny, indicating that the replacement of satellite sequences has occurred in each species lineage independently, and shared variants could not have existed for a long time between species.

Arabidopsis↗

PubMed2005

Characterization of plant Aurora kinases during mitosis.

The Aurora kinase family is a well-characterized serine/threonine protein kinase family that regulates different processes of mitotic events. Although functions of animal and yeast Aurora kinases have been analyzed, plant aurora kinases were not identified and characterized. We identified three Aurora kinase orthologs in Arabidopsis thaliana and designated these as AtAUR1, AtAUR2, and AtAUR3. These AtAURs could phosphorylate serine 10 in histone H3, in vitro. Dynamic analyses of GFP-fused AtAUR proteins revealed that AtAUR1 and AtAUR2 localized at the nuclear membrane in interphase and located in mitotic spindles during cell division. AtAUR1 also localized in the cell plates. AtAUR3 showed dot-like distribution on condensed chromosomes at prophase and then localized at the metaphase plate. At late anaphase, AtAUR3 is evenly localized on chromosomes. The localization of AtAUR3 during mitosis is very similar to that of phosphorylated histone H3. Interestingly, an overexpression of AtAUR3 induces disassembly of spindle microtubules and alteration of orientation of cell division. Our results indicate that plant Aurora kinases have different characters from that of Aurora kinases of other eukaryotes.

Amino Acid Sequence↗

PubMed2004

Interlocus nonrandom association of polymorphisms in Drosophila chemoreceptor genes.

Some forms of multilocus selection with epistasis, such as truncation selection, can effectively reduce the mutation load [Kondrashov, A. S. (1988) Nature 336, 435-440]. Many quantitative characters, including complex genetic diseases, are likely to be subject to these types of selection. However, direct measurement of selection in natural populations is difficult and the effect of epistasis on within-species variations remains unclear. Epistatic interaction in the fitness effect can generate linkage disequilibrium (LD). Therefore, we may detect the action of natural selection from its amount and pattern. Here, we report a large number of interlocus nonrandom associations between polymorphisms in 98 Drosophila chemoreceptor genes. LD was examined in two fly samples collected at the same location, but in different seasons. The amount of LD was much larger in the spring sample than in the autumn one. The between-sample difference was much more striking for the replacement polymorphisms than for the silent polymorphisms. This difference between the replacement and silent polymorphisms could not be attributed to differences in the mean marker distances. We also found a significant excess of associations between one frequent and one less common allele for the replacement polymorphisms, but not for the silent polymorphisms. It is unlikely that a simple seasonal bottleneck could explain all these differences in the scale of LD between the samples and between the replacement and silent polymorphisms. Natural selection is suggested to play a significant role in shaping the pattern of LD observed in this study.

Alleles↗

PubMed2004

Obtaining transgenic plants using the bio-active beads method.

Several methods of transformation are currently available for delivering exogenous DNA into animal and plant cells. In this study, a novel and efficient transformation system for DNA delivery/expression with a capacity to transport DNA of high molecular weight was developed. This system can overcome the shortcomings of traditional transformation methods such as Agrobacterium-mediated transformation, particle bombardment, and the electroporation method. The method developed in this study uses calcium alginate micro beads to immobilize DNA molecules in combination with polyethylene glycol treatment. In addition, it is simple and low-cost, and requires limited equipment. Using this method, we have successfully transformed tobacco plants, screening by kanamycin resistance. The transformed genes in the transformants were confirmed by PCR and Southern hybridization.

Alginates↗

PubMed2003

DNA polymorphism in active gene and pseudogene of the cytosolic phosphoglucose isomerase (PgiC) loci in Arabidopsis halleri ssp. gemmifera.

DNA variations in two PgiC loci were investigated in 15 strains of Arabidopsis halleri ssp. gemmifera. In a 5.5-kb region of the PgiC1 locus, 127 nucleotide substitutions and 33 length variations were observed. In a 6.0-kb region of the PgiC2 locus, 138 nucleotide substitutions and 33 length variations were observed. Frame shift, novel stop codons, and large length variations were observed in the PgiC2 coding region. These findings suggested that PgiC2 may be a pseudogene. The nucleotide diversities (pi) for the entire regions of both PgiC loci were approximately 0.0033. Tajima's test of both PgiC loci yielded significantly negative results. In the coding regions, the high proportions of replacement substitutions caused significant deviations from neutrality in McDonald and Kreitman's test. An excess of singletons and a high proportion of replacement polymorphic sites have been observed in the Adh and ChiA regions of A. halleri ssp. gemmifera. Thus, the A. halleri ssp. gemmifera population may not have reached equilibrium, and thus nonneutral patterns of DNA polymorphism were observed.

Arabidopsis↗

PubMed2003

DNA polymorphism at the ACAULIS5 locus of the wild plant Arabidopsis thaliana.

Nucleotide variation in the ACL5 gene region, which encodes spermine synthase, was analyzed for 21 Arabidopsis thaliana ecotypes and one accession of Arabis gemmifera. In A. thaliana, dimorphism was also detected in the ACL5 region, as in other nuclear genes of this plant. The nucleotide diversity (pi) of the entire region, exon and intron was 0.0163, 0.0042 and 0.0293, respectively. The level of nucleotide variation in this region was among the highest of those reported for genes in this plant species. The neutrality tests of Tajima, and Fu and Li did not detect significant deviation from test assumptions for the polymorphism data. However, the HKA test indicated that the level of polymorphism in the intron was significantly high, compared with A. gemmifera. The high nucleotide variation in the intron is responsible for the high level of nucleotide variation in the entire region. These results can be explained by elevated mutation rate in the ACL5 region in the A. thaliana lineage after the two species were split.

Arabidopsis↗

PubMed2003

Patterns of codon usage bias in three dicot and four monocot plant species.

Codon usage in nuclear genes of four monocot and three dicot species was analyzed to find general patterns in codon choice of plant species. Codon bias was correlated with GC content at the third codon position. GC contents were higher in monocot species than in dicot species at all codon positions. The high GC contents of monocot species might be the result of relatively strong mutational bias that occurred in the lineage of the Poaceae species. In both dicot and monocot species, the effective number of codons (ENCs) for most genes was similar to that for the expected ENCs based on the GC content at the third codon positions. G and C ending codons were detected as the "preferred" codons in monocot species, as in Drosophila. Also, many "preferred" codons are the same in dicot species. Pyrimidine (C and T) is used more frequently than purine (G and A) in four-fold degenerate codon groups.

Amino Acid Sequence↗

PubMed2002

Nucleotide polymorphism at the Atmyb2 locus of the wild plant Arabidopsis thaliana.

DNA variation was studied in a 2.2 kb region of the regulatory gene Atmyb2 using 20 ecotypes of Arabidopsis thaliana and one accession each of Arabis gemmifera and Arabidopsis himalaica. Nucleotide diversity (pi) in the region was 0.0027, which was lower than for other loci in A. thaliana. The MYB domain of the Atmyb2 gene (pi = 0.0036) had a larger variation than the non-MYB region (pi = 0.0013). Tajima's test and Fu and Li's test did not give a significant result. In contrast to the low level of polymorphism, the degree of divergence of the Atmyb2 region was higher between A. thaliana and A. gemmifera (K = 0.0730) than for other loci. The MYB domain (K = 0.0436) had smaller divergence than the non-MYB region (K = 0.0939). The HKA test detected significant discordance in the ratio of polymorphism to divergence in some comparisons. The pattern of low polymorphism and high divergence, which is mainly observed in the non-MYB region of the gene, is inconsistent with the neutral mutation theory. Strong purifying selection after establishment of A. thaliana and a species-specific adaptive process could be invoked to account for this pattern of polymorphism and divergence of Atmyb2.

Arabidopsis↗

PubMed2002

Molecular cloning, sequencing, and chromosome mapping of a 1A-encoded omega-type prolamin sequence from wheat.

Gliadins are the most abundant component of the seed storage proteins in cereals and, in combination with glutenins, are important for the bread-making quality of wheat. They are divided into four subfamilies, the alpha-, beta-, gamma-, and omega-gliadins, depending on their electrophoresis pattern, chromosomal location, and DNA and protein structures. Using a PCR-based strategy we isolated and sequenced an omega-gliadin sequence. We also determined the chromosomal subarm location of this sequence using wheat aneuploids and deletion lines. The gene is 1858 bp long and contains a coding sequence 1248 bp in length. Like all other gliadin gene families characterized in cereals, the omega-gliadin gene described here had characteristic features including two repeated sequences 300 bp upstream of the start codon. At the DNA level, the gene had a high degree of similarity to the omega-secalin and C-hordein genes of rye and barley, but exhibited much less homology to the alpha- and beta-gliadin gene families. In terms of the deduced amino acid sequence, this gene has about 80 and 70% similarity to the omega-secalin and C-hordein genes, respectively, and possesses all the features reported for other gliadin gene families. The omega-gliadin gene has about 30 repeats of the core consensus sequences PQQPX and XQQPQQX, twice as many as other gliadin gene families. Southern blotting and PCR analysis with aneuploid and deletion lines for the short arm of chromosome 1A showed that the omega-gliadin was located on the distal 25% of the short arm of chromosome 1A. By comparison of PCR and A-PAGE profiles for deletion stocks, its genomic location must be at a different locus from gli-Ala in 'Chinese Spring'.

Amino Acid Sequence↗