• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1193-1194
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• 2009

• Bulletin of the Korean Chemical Society
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• 제29권11호
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• pp.2227-2230
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• 2008

• Molecules and Cells
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• 제21권1호
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.

• 생명과학회지
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• 제23권10호
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• pp.1260-1266
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• 2013

본 연구에서는 H. marmoreus 3-10균주와 H. marmoreus 1-1균주의 ribosomal DNA (rDNA) cluster의 분석이 수행되었다. Small subunit (SSU)와 intergenic spacer 2 (IGS 2)는 부분적으로 염기서열이 결정되었고, internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), 5S는 완전하게 염기서열이 결정 되었다. 팽이버섯 H. marmoreus 3-10균주와 H. marmoreus 1-1균주의 rDNA cluster는 총 7,049 bp로 결정되었다. SSU은 1,796 bp, ITS1은 229 bp, 5.8S은 153 bp, ITS2는 223 bp, LSU은 3,348 bp, IGS1은 390 bp, IGS2은 900 bp로 염기서열이 분석되었다. 결정된 rDNA cluster의 총 7,049 bp 중에서 17 bp가 다름이 확인되었고, 각각 SSU (2 bp), ITS (3 bp), LSU (9 bp), IGS (3 bp)에서 차이를 확인하였다. ITS regions의 2차 구조 결과 5개의 stem-loop가 있음이 드러났다. 흥미롭게도, 이들 stem-loop 사이에서 stem-loop V에서 한 개의 상이한 염기가 다른 2차 구조를 나타냄을 확인하였다.

• 미생물학회지
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• 제35권3호
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• pp.211-217
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• 1999

표적 RNA 의 구조가 Tetrahymena thermophila 의 group I intron 에 의한 trans-splicing 반응에 미치는 영향을 분석하기 위해 강력한 stem-loop 형태의 안정된 구조를 갖고 있는 표적 RNA mapping 분석 방법을 이용한 결과 in vitro 뿐만 아니라 in vivo 에서도 stem 부위의 염기들에 반해 loop 부위의 염기들이 ribozyme 에 의해 잘 인지되었으며 이러한 결과는 그러한 부위들을 인지할 수 있는 ribozyme 들에 의한 trans-cleavage 그리고 trans-splicing 반응을 수행함으로써 검증하였다. 또한 이러한 trans-splicing 반응은 정확하게 일어남을 반응 산물의 염기서열 결정을 통해 확인하였다. 따라서 표적 RNA 의 구조가 in vitro 및 in vivo 에서의 ribozyme 활성에 매우 중요한 요인임을 확인하였다.

• 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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• 제41권2호
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• pp.125-128
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• 2005

S. chungbukensis DJ77로부터 16S rRNA유전자의 염기서열을 분식하였다. 염기서열은 총 1,502 bp로 2000 년에 등록된 부분 서열(1,435 bp)보다 5' 방향과 3' 방향으로 29 bp와 37 bp 길이만큼 각각 확장하였으며, 1 bp가 추가로 삽입되었다. E. coli의 16S rRNA유전자를 모델로 이차구조를 제작하였으며, 네 부위가 특이적임을 발견하였다. Sphnigomonas spp.의 16S rRNA 서열과 S. chungbukensis DJ77의 다중서열검색 결과, Sphingomonas종에서만 나타나는 보존부위와 가변부위를 발견할 수 있었다. 특히, Campylobacter jejuni에서만 나타나는 것으로 알려진 긴 stem loop구조가 서열은 조금 다르지만 구조적 일치를 보이는 유사한 구조를 S. chungbukensis DJ77에서도 발견하였다. 결과적으로, 다중서열검색을 통해 제작한 계통수와 nucleotide signatures분석에 근거하여 S. chugukensis DJ77을 cluster II (Sphingobium)로 분류하였다.

• Journal of Applied Biological Chemistry
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• 제42권2호
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• pp.62-65
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• 1999

Iron regulatory proteins (IRPs) 1 and 2 bind with equally high affinity to specific RNA stem-loop sequences known as iron-responsive elements (IRE) which mediate the post-transcriptional regulation of many genes of iron metabolism. To study putative IRE-like sequences in RNA transcripts using the IRP-IRE interaction, Eight known genes from database were selected and the RNA binding activity of IRE-like sequences were compared to IRP-2. Among them, the IRE-like sequence in 3'-untranslational region (UTR) of divalent ration transporter-1 (DCT-1) shows a significant RNA binding affinity. This finding predicts that IRE consensus sequence present within 3'-UTR of DCT-1 might confer the regulation by IRP-2.

• Journal of Microbiology and Biotechnology
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• 제8권1호
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• pp.28-33
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• 1998

A gene coding for ${\beta}$-xylosidase from thermophilic xylanolytic Bacillus sp. KK-1 was cloned into Escherichia coli using plasmid pBR322. Recombinant plasmid DNAs were isloated from E. coli clones which were capable of hydrolyzing 4-methylumbelliferyl-${\beta}$-D xylopyranoside. Restriction analysis showed the DNAs to share a common insert DNA. Xylo-oligosaccharides, including xylotriose, xylotetraose, xylopentaose, and xylobiose were hydrolyzed to form xylose as an end product by cell-free extracts of the E. coli clones, confirming that the cloned gene from strain KK-1 is ${\beta}$-xylosidase gene. The ${\beta}$-xylosidase gene of strain KK-1 designated as xylB was completely sequenced. The xylB gene consisted of an open reading frame of 1,602 nucleotides encoding a polypeptide of 533 amino acid residues, and a TGA stop codon. The 3' flanking region contained one stem-loop structure which may be involved in transcriptional termination. The deduced amino acid sequence of the KK-1 ${\beta}$-xylosidase was highly homologous to the ${\beta}$-xylosidases of Bacillus subtilis and Bacillus pumilus, but it showed no similarity to a thermostable ${\beta}$-xylosidase from Bacillus stearothermophilus.

• Molecules and Cells
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• 제27권4호
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• pp.429-441
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• 2009

We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between $tRNA^{Ser}$(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one $tRNA^{Arg}$-like sequence and one $tRNA^{Lys}$-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.