The insertion sequence element IS8301 isolated from the radiation resistant bacterium Deinococcus radiodurans strain KD8301 was characterized. IS8301 is comprised of 1,736-bp, lacks terminal inverted repeats and does not duplicate target DNA upon its insertion. The amino acid sequence homology of two open reading frames encoded in IS8301 indicates that this insertion sequence element belongs to the IS200/IS605 group. There were seven loci completely identical with the IS8301 sequence in the published D. radiodurans R1 genome sequence. The genome distribution profiles of IS8301 in strain KD8301 as well as in the three different laboratory isolates (KR1, MR1, and R1) of wild-type D. radiodurans were investigated using genomic hybridization analysis. At least 21 strong hybridization signals were detected in strain KD8301 while only one hybridization signal was detected in strain KR1, the parent strain of KD8301. In strain MR1, a different wild-type isolate, six strong hybridization signals were detected. In spite of the identification of seven copies of IS8301 in the published D. radiodurans R1 genome sequence, only one hybridization signal was detected in strain R1 purchased from American Type Culture Collection. Using inverse PCR and sequencing analyses, total 13 different insertion loci of IS8301 in the D. radiodurans genome were identified. Sequence comparison of the flanking region of insertion sites indicated that the sequence 5'-TTGAT-3' preceded the left end of IS8301 in all cases.
Seagrasses are composed of four families belonging to angiosperms and they are thought to become adaptive to aquatic life independently. Zosteraceae is one such family and because of the relatively high species diversity around Japan and Korea coast areas, the family might have arisen therefrom. To elucidate the origin and evolution of Zosteraceae which consists of three genera, Phyllospadix, Zostera, and Heterozostera, 2.8 kb nucleotide sequences of rbcL and matK genes in the chloroplast genome were examined for various species, including cosmopolitan Z. marina and endemic Z. caulescens. The phylogenetic analysis reveals the following three features. First, based on the synonymous nucleotide substitution rate of the rice chloroplast genome, we estimated the divergence times between Zosteraceae and its closest relative, Potamogetonaceae, and between different genera, Zostera and Phyllospadix, as approximately 100 million years (myr) and 36 myr, respectively, suggesting that Zosteraceae emerged somewhere in the period from 36 myr ago to 100 myr ago. Second, two subgenera of Zostera, Zostera and Zosterella, exhibit their reciprocal monophyly and appear to have differentiated from each other approximately 33 myr ago. However, the third genus Heterozostera branched off only 5 myr ago from the stem lineage leading to Zosterella and this seems too recent in comparison with the ancient divergence of the two subgenera. Third, we estimated the most recent common ancestor of subgenus Zostera as 6 myr. In Z. marina four haplotypes were found in the sample and have diversified in the past 1.5 myr. One haplotype is shared by both sides of the Japan Archipelago and its closely related haplotypes occur also in eastern Pacific Ocean. Based on these phylogeographic analyses, we propose a provisional age related classification of Zosteraceae to argue the origin and evolution.
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.
Homeodomain leucine zipper (HD-Zip) genes encode transcription factors that are characterized by both a homeodomain and a leucine zipper motif. Two HD-Zip genes were isolated from cDNA of the male flower bud of the dioecious plant Silenelatifolia. The two isolated genes, SlHDL1 and SlHDL2, encode proteins with the characteristics of HD-Zip transcription factors belonging to HD-Zip classes I and II, respectively. The expression patterns of SlHDL1 and SlHDL2 throughout the floral developmental stages were studied using real-time PCR and insitu hybridization. SlHDL1 is specifically expressed in the outermost layer of the anthers and gynoeciums with a patchy pattern in the inner layers, suggesting that the product of SlHDL1 plays a role in the early developmental stage of the epidermal tissues of these floral organs. Its expression pattern in the anthers and gynoeciums suggests an involvement in differentiation of the reproductive organs. On the other hand, real-time PCR revealed accumulation of SlHDL2 transcripts in the anther and pollen grains of the male flower. These results suggest that SlHDL1 and SlHDL2 regulate specific targets in restricted regions leading to floral organ differentiation in S. latifolia.
rec mutations result in an extremely low level of recombination and a high frequency of primary non-disjunction in the female meiosis of Drosophilamelanogaster. Here we demonstrate that the rec gene encodes a novel protein related to the mini-chromosome maintenance (MCM) proteins. Six MCM proteins (MCM2 - 7) are conserved in eukaryotic genomes, and they function as heterohexamers in the initiation and progression of mitotic DNA replication. Three rec alleles, rec1, rec2 and rec3, were found to possess mutations within this gene, and P element-mediated germline transformation with a wild-type rec cDNA fully rescued the rec mutant phenotypes. The 885 amino acid REC protein has an MCM domain in the middle of its sequence and, like MCM2, 4, 6 and 7, REC contains a putative Zn-finger motif. Phylogenetic analyses revealed that REC is distantly related to the six conserved MCM proteins. Database searches reveal that there are candidates for orthologs of REC in other higher eukaryotes, including human. We addressed whether rec is involved in DNA repair in the mitotic division after the DNA damage caused by methylmethane sulfonate (MMS) or by X-rays. These analyses suggest that the rec gene has no, or only a minor, role in DNA repair and recombination in somatic cells.
To investigate the genetic basis of the seasonal fluctuations in resistance to three organophosphates, observed within a natural population of Drosophila melanogaster (Meigen), we compared the intrinsic rate of increase, generation time and net reproduction rate among chromosome substitution lines derived from a resistant and a susceptible line, obtained from this natural population. There was significant variation among substituted lines; lines possessing the third chromosome from the resistant line, which confers resistance to the three organophosphates, generally showed lower mean values of these fitness measures. Chromosomal analyses also indicated significant negative contributions of the third chromosome from the resistant line. However, significant positive contributions of the interactions among chromosomes from the resistant line to these fitness measures were also detected. We further conducted a local stability analysis, in which each chromosome-substituted line was assumed to be introduced at a low frequency into the initial susceptible population. It was demonstrated that the resistance factor(s) on the third chromosome tend to decrease in their frequency under both density-independent and juvenile density-regulated conditions. Based on these results, a possible explanation for the seasonal fluctuations in resistance to the three organophosphates observed in the natural population was proposed.
The repeating units of the histone gene cluster containing the H1, H2A, H2B and H4 genes were amplified by PCR from the Drosophila melanogaster species subgroup, i.e., D. yakuba, D. erecta,D. sechellia, D. mauritiana, D. teissieri and D. orena. The PCR products were cloned and their nucleotide sequences of about 4.6-4.8kbp were determined to elucidate the mechanism of molecular evolution of the histone gene family. The heterogeneity among the histone gene repeating units was 0.6% and 0.7% for D. yakuba and D. sechellia, respectively, indicating the same level of heterogeneity as in the H3 gene region of D. melanogaster. Divergence of the genes among species even in the most closely related ones was much greater than the heterogeneity among family members, indicating a concerted mode of evolution for the histone gene repeating units. Among the species in the D.melanogaster species subgroup, the histone gene regions as well as 3rd codon position of the coding region showed nearly the same GC contents. These results suggested that the previous conclusion on analysis of the H3 gene regions, the gene family evolution in a concerted fashion, holds true for the whole histone gene repeating unit.