Biomedical subjects

Yoko Satta

Publications and source records attributed to Yoko Satta.

25 records · Page 2Linked to original sources

PubMed2002

Estimation of the highest chromosome number of eukaryotes based on the minimum interaction theory.

According to the minimum interaction theory, the chromosome evolution of eukaryotes proceeds as a whole toward increasing the chromosome number. This raises the following two questions: what was the starting chromosome number of eukaryotes and does the chromosome number increase infinitely? We attempted to provide a theoretical framework to resolve these questions. We propose that the species with n=2 observed in Protozoa, Platyhelminthes, Annelid, Algae, Fungi and higher plants would be chromosomal relicts conserving the karyotypes of ancestral eukaryotes. We also propose that the ideal highest number of eukaryotes (n(max)) can be given by an inverse of the minimum terminal interference distance (It(min)) in crossing-over (n(max)=100/It(min)). AsIt(min) =0.6 in mammals, n(max) approximately 166. On the other hand, the value estimated by computer simulations is somewhat lower with n(max)=133-138. Our arguments can be applied to other eukaryotes, if they have a localized centromere and the ratio of total synaptonemal complex/nuclear volume is comparable to that of mammals. We revealed that the index of gene shuffling per karyotypes (G) by means of the total number of gamete types with different gene combinations can be formulated asG =2(n+Fxi), where Fxi means interstitial chiasma frequency per cell corresponding to crossing-over mediated by the recombination nodule. The Fxi value increases in proportion to the n value in areas where n<40, but decreases gradually when n>40 and becomes zero when n>83. Therefore, in the ultimate karyotype with n(max)=166, FXi=0 andG =2(n)=2(166), where gene shuffling is guaranteed by the random orientation of chromosomes at the equatorial plate of meiotic metaphase I.

Animals↗

PubMed2002

Out of Africa with regional interbreeding? Modern human origins.

A central issue in paleoanthropology is whether modern humans emerged in a single geographic area and subsequently replaced the preexisting people in other areas. Although the study of human mitochondrial DNAs supported this single-origin and complete-replacement model, a recent paper(1) argues that humans expanded out of Africa more than once and regionally interbred. However, both the genetic antiquity and the impact of the African contribution to modern Homo sapiens are so great as to view Africa as a central place of human evolution. Despite the possibility that out-of-Africa H. sapiens interbred with other populations, this evidence is more consistent with the uniregional hypothesis than the multiregional hypothesis of modern human origins.

Africa↗

PubMed2002

Coevolution of the S-locus genes SRK, SLG and SP11/SCR in Brassica oleracea and B. rapa.

Brassica self-incompatibility (SI) is controlled by SLG and SRK expressed in the stigma and by SP11/SCR expressed in the anther. We determined the sequences of the S domains of 36 SRK alleles, 13 SLG alleles, and 14 SP11 alleles from Brassica oleracea and B. rapa. We found three S haplotypes lacking SLG genes in B. rapa, confirming that SLG is not essential for the SI recognition system. Together with reported sequences, the nucleotide diversities per synonymous and nonsynonymous site (pi(S) and pi(N)) at the SRK, SLG, and SP11 loci within B. oleracea were computed. The ratios of pi(N):pi(S) for SP11 and the hypervariable region of SRK were significantly >1, suggesting operation of diversifying selection to maintain the diversity of these regions. In the phylogenetic trees of 12 SP11 sequences and their linked SRK alleles, the tree topology was not significantly different between SP11 and SRK, suggesting a tight linkage of male and female SI determinants during the evolutionary course of these haplotypes. Genetic exchanges between SLG and SRK seem to be frequent; three such recent exchanges were detected. The evolution of S haplotypes and the effect of gene conversion on self-incompatibility are discussed.

Amino Acid Sequence↗

PubMed2002

Persistence of Mhc heterozygosity in homozygous clonal killifish, Rivulus marmoratus: implications for the origin of hermaphroditism.

The mangrove killifish Rivulus marmoratus, a neotropical fish in the order Cyprinodontiformes, is the only known obligatorily selfing, synchronous hermaphroditic vertebrate. To shed light on its population structure and the origin of hermaphroditism, major histocompatibility complex (Mhc) class I genes of the killifish from seven different localities in Florida, Belize, and the Bahamas were cloned and sequenced. Thirteen loci and their alleles were identified and classified into eight groups. The loci apparently arose approximately 20 million years ago (MYA) by gene duplications from a single common progenitor in the ancestors of R. marmoratus and its closest relatives. Distinct loci were found to be restricted to different populations and different individuals in the same population. Up to 44% of the fish were heterozygotes at Mhc loci, as compared to near homozygosity at non-Mhc loci. Large genetic distances between some of the Mhc alleles revealed the presence of ancestral allelic lineages. Computer simulation designed to explain these findings indicated that selfing is incomplete in R. marmoratus populations, that Mhc allelic lineages must have diverged before the onset of selfing, and that the hermaphroditism arose in a population containing multiple ancestral Mhc lineages. A model is proposed in which hermaphroditism arose stage-wise by mutations, each of which spread through the entire population and was fixed independently in the emerging clones.

Alleles↗

PubMed2002

Loss of urate oxidase activity in hominoids and its evolutionary implications.

We have determined and compared the promoter, coding, and intronic sequences of the urate oxidase (Uox) gene of various primate species. Although we confirm the previous observation that the inactivation of the gene in the clade of the human and the great apes results from a single CGA to TGA nonsense mutation in exon 2, we find that the inactivation in the gibbon lineage results from an independent nonsense mutation at a different CGA codon in exon 2 or from either one-base deletion in exon 3 or one-base insertion in exon 5, contrary to the previous claim that the cause is a 13-bp deletion in exon 2. We also find that compared with other organisms, the primate functional Uox gene is exceptional in terms of usage of CGA codons which are prone to TGA nonsense mutations. Nevertheless, we demonstrate rather strong selective constraint against nonsynonymous sites of the functional Uox gene and argue that this observation is consistent with the fact that the Uox gene is unique in the genome and evolutionarily conserved not only among animals but also among eukaryotes. Another finding that there are a few substitutions in the cis-acting element or CAAT-box (or both) of primate functional Uox genes may explain the lowered transcriptional activity. We suggest that although the inactivation of the hominoid Uox gene was caused by independent nonsense or frameshift mutations, the gene has taken a two-step deterioration process, first in the promoter and second in the coding region during primate evolution. It is also argued that the high concentration of uric acid in the blood of humans and nonhuman primates has developed molecular coevolution with the xanthine oxidoreductase in purine metabolism. However, it remains to be answered whether loss of Uox activity in hominoids is related to protection from oxidative damage and the prolonged life span.

Animals↗

PubMed2002

Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates.

Molecular phylogenies of lineages that split from one another in short succession are often difficult to resolve because different loci and different sites within the same locus yield incongruent relationships. The incongruity is commonly attributed to two causes: differential assortment of ancestral polymorphisms and homoplasy. To assess the relative contribution of these two causes, sequences of 57 segments from 51 loci in six primate lineages (human, chimpanzee, gorilla, orangutan, macaque, and tamarin, abbreviated as H, C, G, O, M, and T, respectively) were subjected to "partitioning" analysis, in which phylogenetically informative sites were identified in all 15 pairwise comparisons of each of the 57 segments and tallied for their support or lack thereof for each of the theoretically possible phylogenies. The six lineages include one of the best known cases of a difficult-to-resolve phylogeny: the trichotomy (H, C, G), in which the three lineages may have diverged from each other within a short period of time. In this period many of the ancestral polymorphisms apparently persisted and yielded phylogenetically incongruent signals. By contrast, no ancestral polymorphism is expected to have survived during the interval separating the divergences of the O, M, and T lineages from the ancestor of the (H, C, G) group. Any phylogenetic incompatibilities at sites in the O, M, and T lineages relative to the (H, C, G) group are therefore presumably the result of homoplasy. The frequency of homoplasy estimated in this manner is unexpectedly high: 12% for the (H, C, G) clade and 19% for the (H, C, G, O) clade. At least three-quarters of the 48% incompatibility observed in the (H, C) clade is attributable to the sorting out of ancestral polymorphisms coupled with intragenic recombination. Possible reasons for this high level of homoplasy in the O, M, and T lineages are discussed, and a computer simulation has been carried out to produce a model explaining the observed data.

Animals↗

PubMed2002

The dominance of alleles controlling self-incompatibility in Brassica pollen is regulated at the RNA level.

Self-incompatibility (SI) in Brassica is controlled sporophytically by the multiallelic S-locus. The SI phenotype of pollen in an S-heterozygote is determined by the relationship between the two S-haplotypes it carries, and dominant/recessive relationships often are observed between the two S-haplotypes. The S-locus protein 11 (SP11, also known as the S-locus cysteine-rich protein) gene has been cloned from many pollen-dominant S-haplotypes (class I) and shown to encode the pollen S-determinant. However, SP11 from pollen-recessive S-haplotypes (class II) has never been identified by homology-based cloning strategies, and how the dominant/recessive interactions between the two classes occur was not known. We report here the identification and molecular characterization of SP11s from six class II S-haplotypes of B. rapa and B. oleracea. Phylogenetic analysis revealed that the class II SP11s form a distinct group separated from class I SP11s. The promoter sequences and expression patterns of SP11s also were different between the two classes. The mRNA of class II SP11, which was detected predominantly in the anther tapetum in homozygotes, was not detected in the heterozygotes of class I and class II S-haplotypes, suggesting that the dominant/recessive relationships of pollen are regulated at the mRNA level of SP11s.

Alleles↗