• Microbiology and Biotechnology Letters
• /
• v.20 no.6
• /
• pp.619-624
• /
• 1992

Tn5 lac 삽입으로 채소입고병원균에 길항력이 약화된 T-67 및 고추역병균과 참깨역병균에 길항력이 약화된 T-81의 Tn5 lac 유전자 일부와 오른쪽 말단에 있는 길항관련 유전자의 flanking sequence가 cloning된 pAG67 및 pAG81 clone을 선발하였고, pAG67 및 pAG81 clone된 길항관련 유전자의 flanking sequence를 야생 길항균 Pseudomonas maltophilia B-14의 DNA를 probe로 사용하여 Southern hybridization으로 확인하였으며, 제한효소 지도를 작성하여 8Kb 및 4Kb 크기의 flanking sequence가 cloning되었음을 확인하였다. pAG6 및 pAG81의 flanking sequence를 EcoRi-BglII와 EcoRI-MpaI으로 분리하여 유전자 은행으로부터 길항관련 유전자가 cloning된 cosmid clone 7개주를 선발하였다.

• Journal of Microbiology and Biotechnology
• /
• v.12 no.4
• /
• pp.622-627
• /
• 2002

Diphtheria toxin repressor (DtxR) binds to approximately 30 to 35-bp regions containing an interrupted 9-bp inverted repeat within a 19-bp core sequence. The core sequence is fairly conserved and critical for DtxR binding. The flanking regions that are consisted of 5 to 8 more of nucleotides from the core are also required for DtxR binding. The nucleotides in both flanking regions are A-T rich. To examine whether the A-T nucleotides in both flanking regions from the core have significant roles for DtxR binding, a DNA fragment was constructed based on the diphtheria tox promoter/operator, and DNA fragments with substitution of A and T nucleotides In the flanking regions to G and C were also constructed. To assess the effect of these substitutions on binding of DtxR and repressibility by DtxR, $\beta$-galactosidase activity from lacZ fused to the region was assessed. Gel mobility shift of the region by purified DtxR was also examined. The DNA fragments containing the mutations in the flanking regions still exhibited repression and mobility shift with DtxR. The core segment with the mutation is still, therefore, recognized by DtxR. Nonetheless, the results from the assays indicated that the substitution significantly decreased repression of the operator by DtxR in vivo under high-iron condition and decreased binding of DtxR to the operator. These results suggest that A and T nucleotides fur both flanking regions are preferred for the binding of DtxR.

• Journal of Plant Biology
• /
• v.33 no.4
• /
• pp.303-307
• /
• 1990

A genomic clone carrying a proteinase inhibitor I sequence was isolated and characterized. The clone contained a 0.7 kb EcoRI fragment hybridized with tomato inhibitor I cDNA. The nucleotide sequence of the EcoRI fragment revealed presence of a truncated form of a proteinase inhibitor I gene of potato. The truncated gene contained the 5' flanking region and the first exon of a functional proteinase inhibitor I gene. Although the 5' flanking region contained the regulatory sequences TATAAA and CCACT, a deletion of 40 bp occurred between them.

• Journal of Microbiology
• /
• v.42 no.1
• /
• pp.56-59
• /
• 2004

Together with the previous reports, my computer survey revealed that several bacteria contain six copies of the type group II intron IntA. The sequence analysis of IntAs showed the high level of homology in the nucleotide sequence (91.9-99.8%). The consensus sequence, 2,270 base pair long, was derived from the nucleotide sequences of all IntA members. The size of the open reading frame intA was 502 amino acids long, that is homologous to reverse transcriptase-like proteins encoded within the group II introns. It was reported that EPEC.IntA and Sf.IntA were inserted into IS911 and IS629, respectively. The sequence of the flanking region IntA was analyzed here. The data show the insertion of EC.IntA into IS629, the insertion of EHEC.IntA into IS3, the insertion of Yp.IntA into IS904-like sequence, and the insertion of EK12.IntA into IS911. Interestingly, these IS elements nested by IntAs were the members of IS3 family elements. The sequences of the IS3 members correspond to the OrfB with the DDE motif conserved in retroviral integrases. Alignment of the flanking sequences of IntAs revealed that the flanking regions -25 to + 10 of insertion sites, that are generally believed to be required for the retrohoming, were not strongly conserved. The data presented here suggests that the retrohoming pathway of IntA seems to differ from those of other group II introns.

• Genomics & Informatics
• /
• v.5 no.2
• /
• pp.68-76
• /
• 2007

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

• Development and Reproduction
• /
• v.7 no.2
• /
• pp.119-126
• /
• 2003

In the previous study, we obtained list of differentially expressed genes between postnatal day 1 and day 5 mouse ovaries using suppression subtractive hybridization(SSH) and found that MT Oansposon-like element, clone MTi7(MTi7) was one of the highly expressed genes in the day 5 mouse ovary(Park et at., 2002). Results of in situ hybridization and RNA interference revealed that the expression of MTi7 is oocyte-specific in the ovary and may be involved in the regulation of oocyte maturation(Park et at., 2003). At present, MTi7 sequence has been known only in the mouse. Therefore, the present study was accomplished 1) to identify MTi7 sequence in the other mammalian species, such as bovine, porcine, rat, and human, and 2) to evaluate the flanking sequence of the mouse MTi7 since it has transposon characteristics. Using ovarian cDNAs derived from low different species, we cloned and identified new MTi7 sequence showing a high degree of sequence homology with the mouse MTi7(87∼98%). By using inverse PCR, we found that the mouse MTi7 may intercalated the beta-carotene 15, 15'-monooxygenase(Bcdo) gene and/or serine protease inhibitor, Kunitz Dpe I(Spint 1) gene. By finding the MTi7 sequences in the other mammalian species and the flanking gene of the MTi7 in mouse, it is expected to reveal the role(s) of MTi7 in the oogenesis as well as folliculogenesis in the near future.

• Korean Journal of Microbiology
• /
• v.30 no.6
• /
• pp.488-494
• /
• 1992

Three clones containing mouse CD4 gene were prepared using AKR genomic cosmid library. The role of 6, 500 bp 5' flanking region of the first exon of the AKR CD4 gene in tissue or developmental stage specific expression of CD4 has been studied. The deletion constructs containing various amounts of CD4 5' flanking sequences were prepared, and they were transfected into the cell lines representing different cell types or developmental stages of CD4 expression. Study of the reporter gene expression revealed that at least 1, 700 bp of 5' flanking region did retain promoter activity for CD4 expression. This area did not seem to contain enhancer activity for a full expression of CD4. However, the putative promoter interacted with other tissue specific enhancer sequence and showed the tissue specificity of the enhancer element.

• Horticultural Science & Technology
• /
• v.29 no.2
• /
• pp.123-129
• /
• 2011

To identify unintended vertical gene-transfer rates from the developed transgenic plants, rapid and unequivocal techniques are needed to identify event-specific markers based on flanking sequences around the transgene and to distinguish zygosity such as homo- and hetero-zygosity. To facilitate evaluation of zygosity, a polymerase chain reaction technique was used to analyze a transgenic pepper line B20 (homozygote), P915 wild type (null zygote), and their F1 hybrids, which were used as transgene contaminated plants. First, we sequenced the 3'-flanking region of the T-DNA (1,277 bp) in the transgenic pepper event B20. Based on sequence information for the 3'- and 5'-flanking region of T-DNA provided in a previous study, a primer pair was designed to amplify full length T-DNA in B20. We successfully amplified the full length T-DNA containing 986 bp from the flanking regions of B20. In addition, a 1,040 bp PCR product, which was where the T-DNA was inserted, was amplified from P915. Finally, both full length T-DNA and the 1,040 bp fragment were simultaneously amplified in the F1 hybrids; P915 ${\times}$ B20, Pungchon ${\times}$ B20, Gumtap ${\times}$ B20. In the present study, we were able to identify zygosity among homozygous transgenic event B20, its wild type P915, and hemizygous F1 hybrids. Therefore, this novel zygosity identification technique, which is based on PCR, can be effectively used to examine gene flow for transgenic pepper event B20.

• BMB Reports
• /
• v.42 no.12
• /
• pp.788-793
• /
• 2009

TLX2 is an orphan homeodomain transcription factor whose expression is mainly associated with tissues derived from neural crest cells. Recently, we have demonstrated that PHOX2A and PHOX2B are able to enhance the neural cell-type specific expression of human TLX2 by binding distally the 5' -flanking region. In the present work, to deepen into the TLX2 transcription regulation, we have focused on the proximal 5'-flanking region of the gene, mapping the transcription start site and identifying a minimal promoter necessary and sufficient for the basal transcription in cell lines from different origin. Site-directed mutagenesis has allowed to demonstrate that the integrity of this sequence is crucial for gene expression, while electrophoretic mobility shift assays and chromatin immunoprecipitation experiments have revealed that such an activity is dependent on the binding of a PBX factor. Consistent with these findings, such a basal promoter activity has resulted to be enhanced by the previously reported PHOX2-responding sequence.

• Microbiology and Biotechnology Letters
• /
• v.13 no.1
• /
• pp.19-25
• /
• 1985

The HIS5 gene of Saccharomyces cerevisiae host was encoded histidinol phosphate aminotransferase(E.C.: 2.6. 1.9). The HIS5 gene of Saccharomyces cerevisiae was cloned on plasmid pSH 530. This gene mighted be transcripted from a promoter of yeast gene both in E. coli and yeast hosts. We have determined the nucleotide sequence of the yeast HIS5 gene and its 5' and 3' flanking sequences. There are no large differences between the relative levels of HIS5 mRNA molecules with different 5' termini in represent and derepressed cell. In the DNA sequence upstream from the 5' termini of HIS5 mRNA we have found live closely related copies of a 9 base pair sequence. The sequence is also repeated in the 5' noncoding regions of HIS1, HIS3, HIS4, HIS5 and TRP5. Closely related sequence are not found flanking repeat sequence plays a role in the regulation of amino acid biosynthetic genes subject to the general amino acid control.