• 한국식물학회:학술대회논문집
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• 한국식물학회 1987년도 식물생명공학 심포지움 논문집 Proceedings of Symposia on Plant Biotechnology
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• pp.391-401
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• 1987

Plant chloroplast DNA exists as an unique circular structure in which large single copy(LSC) region and small single copy (SSC) region are separated by large inverted repeat sequences (IRS). It has been known that the unique existence of inverted repeat sequences in chloroplast DNA has no relation with the stability of the chloroplast DNA, but causes the inversion between inverted repeat its biological significance has not been understood so far. In rice, several gene clusters have been cloned and sequenced which contain ribulose-5-biophosphate car-boxylase large subunit (rbcL). Especially, one rbcL gene is linked with rp12 gene which is located in the IRS region in one of the gene clusters. By comparison of nucleotide sequence, the two genes are found to be linked through 151 bp repeat sequence which is homologous to the rp123 gene in IRS region. The repeat sequence is found to be located 3' downstream of rfcL gene and near psbA gene in LSC region. The existence of these repeat sequences and the presence of gene clusters caused by the gene rearrangement thorough the repeat sequence provide a possible which is found to be dispersed chloroplast DNA provide the model system to explaine the heterogeneity of the chloroplast DNA in rice in term of gene rearrangement.

• Molecules and Cells
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• 제26권4호
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• pp.387-395
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• 2008

A novel Tc1-like transposable element has been identified as a new DNA transposon in the mud loach, Misgurnus mizolepis. The M. mizolepis Tc1-like transposon (MMTS) is comprised of inverted terminal repeats and a single gene that codes Tc1-like transposase. The deduced amino acid sequence of the transposase-encoding region of MMTS transposon contains motifs including DDE motif, which was previously recognized in other Tc1-like transposons. However, putative MMTS transposase has only 34-37% identity with well-known Tc1, PPTN, and S elements at the amino acid level. In dot-hybridization analysis used to measure the copy numbers of the MMTS transposon in genomes of the mud loach, it was shown that the MMTS transposon is present at about $3.36{\times}10^4$ copies per $2{\times}10^9$ bp, and accounts for approximately 0.027% of the mud loach genome. Here, we also describe novel MMTS-like transposons from the genomes of carp-like fishes, flatfish species, and cichlid fishes, which bear conserved inverted repeats flanking an apparently intact transposase gene. Additionally, BLAST searches and phylogenetic analysis indicated that MMTS-like transposons evolved uniquely in fishes, and comprise a new subfamily of Tc1-like transposons, with only modest similarity to Drosophila melanogaster (foldback element FB4, HB2, HB1), Xenopus laevis, Xenopus tropicalis, and Anopheles gambiae (Frisky).

• Journal of Microbiology and Biotechnology
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• 제18권6호
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• pp.1033-1039
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• 2008

A 3-kb HindIII fragment bearing the cry6Aa2 gene and the adjacent and intergenic regions was cloned from Bacillus thuringiensis strain YBT-1518. Two open reading frames (ORFs), namely, orf1 (termed cry6Aa2) and orf2 that were separated by an inverted-repeat sequence were identified. orf1 encoded a 54-kDa protein that exhibited high toxicity to the plant-parasitic nematode Meloidogyne hapla. The orf2 expression product was not detected by SDS-PAGE, but its mRNA was detected by RT-PCR. The orf2 coexpressed with orf1 at a high level in the absence of the inverted-repeat sequence, whereas, the expression level of otfl was decreased. When orf2 was mutated, the level of orf1 expression was enhanced obviously. In conclusion, the inverted-repeat sequence disturbs orf2 expression, and the orf2 downregulates orf1 expression. This is an example of novel negative regulation in B. thuringiensis and a potential method for enhancing the expression level of cry genes.

• 식물분류학회지
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• 제53권3호
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• pp.230-236
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• 2023

Rhododendron caucasicum Pall. is a shrub distributed in the mountainous areas of the Caucasus from northeastern Türkiye towards the Caspian Sea. This study reports the first complete chloroplast genome sequence of R. caucasicum. The plastome is 199,487 base pairs (bp) long and exhibits a typical quadripartite structure comprising a large single-copy region of 107,645 bp, a small single-copy region of 2,598 bp, and a pair of identical inverted repeat regions of 44,622 bp each. It contains 143 genes, comprising 93 protein-coding genes, 42 tRNA genes, and eight rRNA genes. The large chloroplast genome size is likely due to the expansion of inverted repeats. A phylogenetic analysis of chloroplast genomes with other Rhododendron species supports previously recognized infrageneric relationship.

• BMB Reports
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• 제40권3호
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• pp.404-411
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• 2007

Transformation of cantaloupes with the coat protein (cp) gene of papaya ringspot virus type W (PRSV-W), Thai isolate, was used to introduce virus resistance. Binary vectors containing either the full length coat protein coding region under control of the 35S CaMV promoter(pSA1175), or the inverted-repeat of a coat protein coding region (pSA1304), were constructed and used for Agrobacteriummediated transformation of cotyledonary explants of the cantaloupe cultivar Sun Lady. Four independent transgenic lines were obtained using pSA1304 and one using pSA1175. Integration of the PRSV-W cp gene into the genome of these transgenic lines was verified by PCR amplification, GUS assays and Southern blot hybridization. In vitro inoculation of these lines with PRSV-W revealed that whereas the line containing pSA1175 remained sensitive, the four lines containing pSA1304 were resistant. The presence of small RNA species, presumably siRNA, corresponding to regions of the viral cp gene in transgenic lines resistant to PRSV-W supports the involvement of post-transcriptional gene silencing in the establishment of resistance.

• Journal of Plant Biotechnology
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• 제46권4호
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• pp.323-330
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• 2019

The high expression level of industrial and metabolically important proteins in plants can be achieved by plastid transformation. The CaIA vector, a Capsicum-specific vector harboring aadA (spectinomycin resistance), is a selectable marker controlled by the PsbA promoter, and the terminator is flanked by the trnA and trnI regions of the inverted repeat (IR) region of the plastid. The CaIA vector can introduce foreign genes into the IR region of the plastid genome. The biolistic method was used for chloroplast transformation in Scoparia dulcis with leaf explants followed by antibiotic selection on regeneration medium. Transplastomes were successfully screened, and the transformation efficiency of 3 transgenic lines from 25 bombarded leaf explants was determined. Transplastomic lines were evaluated by PCR and Southern blotting for the confirmation of aadA insertion and its integration into the chloroplast genome. Seeds collected from transplastomes were analyzed on spectinomycin medium with wild types to determine genetic stability. The increased chloroplast transformation efficiency (3 transplastomic lines from 25 bombarded explants) would be useful for expressing therapeutically and industrially important genes in Scoparia dulcis L.

• Journal of Microbiology
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• 제37권4호
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• pp.229-233
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• 1999

The mitochondrial plasmid pMLP1 from a white-rot fungus, Pleurotus ostreatus, is a double-stranded DNA containing 381 bp terminal inverted repeat (TIR) whose 5'-ends are covalently bound by terminal proteins. The plasmid contains two major open reading frames (ORFs), encoding putative DNA and RNA polymerases, and a minor ORF encoding a small, highly basic protein. To identify the DNA binding activity that recognizes the TIR region of pMLP1, gel retardation assays were performed with mitochondrial extracts. A specific protein binding to a region between 123 and 248 nt within TIR was observed. We examined whether the gene product of mORF1 bindes to this region specifically. E. coli cell extract which contains an overproduced mORF1 protein formed a complex specific to the region between 123 and 248 nt. Inclusion of mORF1 protein in the specific complex formed between P. ostreatus mitochondrial extract and TIR was confirmed by a supershift assay using polyclonal antibodies against the mORF1 protein. Our result suggest that the product of mORF1 may function as a terminal region recognition factor (TRF), recognizing an internal region in TIR.

• Molecules and Cells
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• 제19권1호
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• pp.104-113
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• 2005

Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.

• 미생물학회지
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• 제40권2호
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• pp.65-72
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• 2004

진핵생물의 특정 염기배열을 원핵생물 내에서 증폭시킬 때 불안정성이 비교적 빈번히 관찰되어진다. 특히 long inverted repeats나 AT-rich sequences그리고 Z-DNA와 같은 구조를 지닌 염기배열은 대장균 내에서 매우 불안정하다. 이러한 염기서열은 대장균 내에서 부분적으로 결실되거나 완전히 손실된다. 본 연구실에서 human SCKI 유전자에 존재하는 몇 개의 tandem repeat (TR)에 대하여 다형성을 조사하였을 때, 어떤 TR 부분은 플라스미드로부터 빈번히 결실되어 그에 대한 염기서열 결정이 어려웠다. 그 결과 이러한 부분은 클론닝 될 수 없는 염기서열로 남게 되었다. 본 연구에서는 클론닝이 어려운 두 개의 TR 영역을 저온에서 클론닝하고 nebulizer나 sonicator를 이용하여 두 개의 library를 만들어 DNA 염기서열을 결정하였다. 이러한 연구는 복잡한 고등생물의 게놈연구에서 불안정한 게놈부분의 염기서열을 결정하는데 도움을 줄 것으로 사료된다.

• Genomics & Informatics
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• 제4권4호
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• pp.167-169
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• 2006

PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user-defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users.