Sachiko Ichimura

Highly repetitive structure and its organization of the silk fibroin gene

We have sequenced a number of cDNAs representing the Bombyx mori silk fibroin heavy chain transcript. These reveal that the central region of the fibroin gene is composed of alternate arrays of the crystalline element a and the noncrystalline element b. The core region is partitioned by a homogeneous nonrepetitive amorphous domain of around 100 by in length. The element a is characterized by repeats of a highly conserved 18-bp sequence coding for perfect repeats of the unit peptide Gly-Ala-Gly-Ala-Gly-Ser. The element b is composed of repeats of a less-conserved 30-bp sequence which codes for a peptide similar to that in element a except in that (1) Ser is replaced by Tyr and (2) there are irregular substitutions of Ala to Val or Tyr. Therefore, the structure of the fibroin gene core consists of three-step higher-order periodicities. Heterogeneities in numbers of repeats are observed in each step of periodicity. Boundary sequence appeared in each periodicity to be quite homogeneous. Sequence analysis indicates that the unit sequences of elements a and b have homology to those of recombination hotspots reported in other genes and a recombination event may frequently occur between the misaligned sister chromatids, resulting in heterogeneities in repeat numbers and duplication or deletion of repetitive sequences. The repetitive superstructure of the fibroin gene may have been a result of continuous unequal crossovers in a primordial gene during evolution. A couple of important features of the fibroin protein were proved by the present nucleotide sequencing. The amino acid representation of the amorphous domain is vastly different from that of the repetitive regions. The carboxy-terminal nonrepetitive region has three Cys and nine (Arg + Lys) residues that may be responsible for complex formation with the fibroin light-chain molecule. The present DNA analysis also clearly demonstrates that the tRNA population in the posterior silk gland strictly complements the frequency of codons in the fibroin mRNA, which may help to achieve a highly efficient translation of fibroin mRNA.

Specifie codon usage pattern and its implications on the secondary structure of silk fibroin mRNA

We have identified two distinctive regions of the repetitive unit nucleotide sequence of fibroin mRNA of Bombyx mori. The codon usage for the major amino acids, glycine, alanine and serine is distinctly different in these two regions, indicating that it is determined by the fibroin mRNA or gene structure but not by the tRNA population. Comparative computer analyses of nucleotide substitutions in the unit sequence suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the fibroin mRNA.

Quantitative determination of single-stranded sections in DNA using the fluorescent probe acridine orange

Abstract A method for the quantitative determination of single-stranded sections in DNA was developed. Fractions of denatured sections can be estimated using a suitable calibration curve which is obtained on the basis that acridine orange bound to denatured DNA emits a weaker fluorescence at 530 nm and a stronger one at 640 nm than does the dye bound to native DNA. The most suitable conditions, where dye is bound to both types of DNA with the same efficiency, were determined to be an ionic strength of 0.01 and a DNA phosphate to bound dye ratio of 7.5. Under these conditions, the fluorescence intensity at 530 nm of the dye added to the mixture of native and heat-denatured DNA decreased linearly as the fraction of denatured DNA increased. In relation to making a calibration curve, the conformation of heat-denatured calf thymus DNA at an ionic strength of 0.01 was studied. When heated DNA was chilled, only a few percent of total nucleotides reformed the double helical structure in spite of the considerable decrease in hyperchromicity.

The nature of strong binding between acridine orange and deoxyribonucleic acid as revealed by equilibrium dialysis and thermal renaturation.

Abstract The strong binding of acridine orange with DNA was studied by means of equilibrium dialysis and thermal renaturation of the complex. Thermodynamic parameters for the strong binding with native and denatured DNA were calculated from the data of equilibrium dialysis. The association constant and the change of free energy were nearly equal for both types of DNA, but the changes of enthalpy and entropy were quite different. Binding to both types of DNA may be strong binding in nature, but the accompanying effects on the secondary structures of DNA would be different. It was found that the presence of acridine orange inhibits the completion of renaturation, presumably due to a stabilizing effect of the bound dye on the “wrong” base pairs as they are formed. The results support the notion that binding of acridine orange with the double helix is an intercalation into adjacent base pairs, while the binding with single strand is a partial intercalation into adjacent bases.

Early Induction of CDKN1A (p21) and GADD45 mRNA by a Low Dose of Ionizing Radiation is due to Their Dose-Dependent Post-transcriptional Regulation

Abstract Daino, K., Ichimura, S. and Nenoi, M. Early Induction of CDKN1A (p21) and GADD45 mRNA by a Low Dose of Ionizing Radiation is due to Their Dose-Dependent Post-transcriptional Regulation. Radiat. Res. 157, 478–482 (2002). Previous studies have shown that induction of some genes by low-dose radiation has a different dependence on the time after irradiation than induction by high doses. To examine the mechanisms underlying this phenomenon, we investigated the changes in the time course of the rates of transcription of genes in cells of the human myeloblastic leukemia cell line ML-1 by a nuclear run-on assay. It is possible that the more rapid induction of the mRNA of the CDKN1A and GADD45 genes after exposure to 50 cGy of X rays than after 20 Gy is due to a lower level of stabilization of the mRNA of these genes after 50 cGy. In addition, our results show that 50 cGy of X rays increases the transcription rates of the CDKN1A and GADD45 genes, with a maximum induction at 0.5 to 1 h after irradiation, much earlier than the maximum accumulation of stabilized TP53 protein. We suggest the involvement of BRCA1 protein in the early induction of transcription of these two genes.

Phosphatidylinositol 3-kinase inhibitors, Wortmannin or LY294002, inhibited accumulation of p21 protein after γ-irradiation by stabilization of the protein

Expression of the cyclin kinase inhibitor, p21, is regulated both transcriptionally and posttranscriptionally by the ubiquitin-proteasome degradation pathway. Recently, we reported that DNA damage is required for efficient p21 expression by demonstrating that enhanced p21 mRNA expression induced by DNA damage results in increased p21 protein, but enhanced p21 mRNA without DNA damage does not. In addition, we demonstrated that DNA damage suppressed the ubiquitination of p21. In this study, we analyze the link between p21 stabilization and DNA damage. Enhanced p21 protein expression in ML-1 cells resulting from 15 Gy gamma-irradiation was diminished by Wortmannin or LY294002 pretreatment of cells. However, the levels of p21 mRNA were not affected by inhibitor pretreatment. Wortmannin or LY294002 pretreatment reduces p53 expression after gamma-irradiation to a lesser degree than that of p21. In addition, we examined the involvement of DNA-PK, whose activity is inhibited by Wortmannin or LY294002, in p21 stabilization using the SCID fibroblast cell line and a DNA-PK targeting ML-1 cell line. Accumulation of p21 protein by gamma-irradiation was similar to that of DNA-PK intact cells and was reduced by Wortmannin or LY294002 pretreatment. Involvement of another DNA damage detecting enzyme, the ATM gene product, whose activity is also inhibited by Wortmannin or LY294002, was evaluated. ATM deficient cells induced p21 after gamma-irradiation, gamma-irradiation-induced p21 protein was diminished by pretreatment of cells with Wortmannin or LY294002. We conclude that the p21 stabilization mechanism functions after gamma-irradiation, was sensitive to Wortmannin or LY294002, and required neither DNA-PK nor ATM gene product for activity.

HETEROGENEOUS STRUCTURE OF THE POLYUBIQUITIN GENE UBC OF HELA S3 CELLS

The nucleotide sequence of the polyubiquitin gene UbC of HeLa S3 cells and its upstream region was determined and characterized. Recognition sequences for the transcription factors HSF, NF kappa B, AP-1(c-jun), NF-IL6 and Sp1 were found in the upstream control region, a result consistent with the observation of a distinct regulatory response for the UbC gene compared with that of another polyubiquitin gene UbB. Employing a PCR procedure to amplify the entire coding region from genomic DNA, we found a heterogeneity in the repeat number (eight and nine repeats) of the ubiquitin coding units, which resulted from an apparent deletion of either the seventh or the eighth unit in the predominant nine-ubiquitin-unit coding gene. In addition, by comparison with the nucleotide sequence of the UbC gene of human leukocytes previously determined, we found a significant number of nucleotide discrepancies. However, these discrepancies could be substantially reduced by realigning the units so that the first and second ubiquitin units of the sequence determined here are translocated to the boundary between the eighth and the ninth units.

Difference between polylysine and polyarginine in changing DNA structure upon complex formation

Abstract Soluble complexes of DNA with poly-L-lysine and poly-L-arginine were prepared by dialysis or mixing method, and their circular dichroism spectra and viscosities were measured. Both complexes formed by dialysis method had different circular dichroism spectra from that of free DNA respectively, i.e., the spectrum of the DNA-poly-L-lysine complex was similar to that of DNA at high salt concentration and the spectrum of the DNA-poly-L-arginine complex resembled that of DNA under melting at elevated temperature. The viscosity of the both complexes decreased pronouncedly with the increase in peptide to DNA ratio, although the viscosity of the DNA-poly-L-lysine complex was more rapidly decreased than that of the DNA-poly-L-arginine complex. The difference between the two polypeptides in changing DNA structure was observed also in the complexes formed by mixing method.

A MAJOR NON-LTR RETROTRANSPOSON OF BOMBYX MORI, L1BM

Abstract. Repetitive sequences with oligo A tails were observed in Dra1 fragments of Bombyx mori genomic DNA. The full sequence of the element, an abundant non-LTR retrotransposon of B. mori, was determined by assembling inner restriction fragments. This element, designated L1Bm, contained two ORFs encoding a gag-like protein and reverse transcriptase (RT), respectively. An endonuclease domain was identified at the N-terminus of the RT sequence. The homology search of the amino acid sequences revealed that L1Bm belongs evolutionally to the same family as various other non-LTR retrotransposons of Drosophila and Mosquito. On the other hand, L1Bm resembles the L1 element of human genome in its high copy number and its frequent truncation at the 5′-side. Some units of the histone gene repeat in B. mori possess complete L1Bm elements in a 3′-flanking region of H2b.

Identification of the regulatory region required for ubiquitination of the cyclin kinase inhibitor, p21.

The expression of cyclin kinase inhibitor p21 is regulated by the ubiquitin-proteasome protein degradation system, as well as by transcriptional regulation. Generally, ubiquitination is regulated by the phosphorylation of the substrate. In this study, we identified the region of p21 responsible for the regulation of ubiquitination. Since the phosphorylation sites of p21 are distributed in the C-terminal region, we constructed sequential C-terminal truncated fragments and examined their ubiquitination in eukaryotic cells. The ubiquitination was observed in the 1-164 (full length) and 1-157 fragments with the same efficiency, but not in the 1-147 fragment. The lack of ubiquitination in the 1-147 fragment was unlikely due to the removal of a Lys residue at position 154, since the p21 K154R mutant was ubiquitinated as efficiently as the full-length p21. Furthermore, the 148-157 deleted form of p21 was not ubiquitinated, just like the 1-147 fragment. Thus, the C-terminal 148-157 region, not a ubiquitination site by itself, should contain an essential regulatory region for the efficient ubiquitination of p21.