• Mycobiology
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• v.42 no.2
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• pp.167-173
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• 2014

A ${\beta}$-glucan synthase gene was isolated from the genomic DNA of polypore mushroom Sparassis crispa, which reportedly produces unusually high amount of soluble ${\beta}$-1,3-glucan (${\beta}$-glucan). Sequencing and subsequent open reading frame analysis of the isolated gene revealed that the gene (5,502 bp) consisted of 10 exons separated by nine introns. The predicted mRNA encoded a ${\beta}$-glucan synthase protein, consisting of 1,576 amino acid residues. Comparison of the predicted protein sequence with multiple fungal ${\beta}$-glucan synthases estimated that the isolated gene contained a complete N-terminus but was lacking approximately 70 amino acid residues in the C-terminus. Fungal ${\beta}$-glucan synthases are integral membrane proteins, containing the two catalytic and two transmembrane domains. The lacking C-terminal part of S. crispa ${\beta}$-glucan synthase was estimated to include catalytically insignificant transmembrane ${\alpha}$-helices and loops. Sequence analysis of 101 fungal ${\beta}$-glucan synthases, obtained from public databases, revealed that the ${\beta}$-glucan synthases with various fungal origins were categorized into corresponding fungal groups in the classification system. Interestingly, mushrooms belonging to the class Agaricomycetes were found to contain two distinct types (Type I and II) of ${\beta}$-glucan synthases with the type-specific sequence signatures in the loop regions. S. crispa ${\beta}$-glucan synthase in this study belonged to Type II family, meaning Type I ${\beta}$-glucan synthase is expected to be discovered in S. crispa. The high productivity of soluble ${\beta}$-glucan was not explained but detailed biochemical studies on the catalytic loop domain in the S. crispa ${\beta}$-glucan synthase will provide better explanations.

• Korean Journal of Microbiology
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• v.31 no.3
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• pp.197-202
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• 1993

The budding yeast S. cerevisiae contains 10-nm filament ring that lies just inside the plasma memhrane in the region of the mother-bud neck. It is possihle that CDC3. CDCIO, CDCII. CDCI2 genes encode the filaments. Recently it has been shown that the CDC3 and CDCI2 gene products arc localized to [he vicinity of the neck lilaments by immunolluorescence. However. the role of the lilament ring is not clear. In order to find out the role of filament ring. I have tried to clone the similar gene in S. pomhe to the CDC3 in S. cerevisiae. Genomic library was constructed by use of $\lambda$gtll expression vector and screened with CDC3 antibodies. From sequencing data, there were more than two introns in the newly cloned gene. There was 62% homology between the part of the predicted amino acid sequence of cloned gene and CDC3 amino acid sequence.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.7
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• pp.3073-3077
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• 2015

Background: TP53 mutations are the most common genetic alterations in human cancers. There are also several polymorphisms in both exons and introns of TP53 that may influence its anti-tumor functions and increase the risk of cancer development. Associations of the TP53 intron 6 G13964C polymorphism with increased risk of development of several cancers have been investigated in numerous studies, but the results were controversial and conflicting. In this study, we aimed to investigate the probable association of this polymorphism with risk of both thyroid and breast cancers among the Iranian-Azeri population. Materials and Methods: We performed two separate case control studies on associations of the intron 6 polymorphism with two different kinds of cancer. In one case-control study, a total of 75 patients with thyroid carcinoma and 180 controls were analyzed and the other study included 170 patients with breast cancer and 135 healthy women. The intron 6 genotype was determined by RFLP-PCR and the SPSS 16 program was applied for data analysis. Results: For thyroid cancer, the frequencies of GG genotype were 96.0% in patients and 93.3% in controls. The GC genotype had a frequency of 4.0 % in patients and 6.7% in controls. In the study on breast cancer, the frequency of GG and GC genotypes in patients were 95.3% and 4.7%, respectively. In breast related control group, the frequency of GG genotype was 93.3 % and the frequency of GC genotype was 6.7%. None of the cases and controls had the CC genotype. Conclusions: There was no significant association between the TP53 intron 6 G13964C polymorphism and risk of development of both thyroid and breast cancer in Iranian-Azeri patients.

• KSBB Journal
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• v.31 no.4
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• pp.193-199
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• 2016

Global warming caused from the heavy consumption of fossil fuel is one of the biggest problems to be solved. Biofuel has been gained more attention as an alternative to reduce the consumption of fossil fuel. Recently, butanol produced from the genus Clostridium has been considered as one of the promising alternatives for gasoline, fossil based fuel. Nevertheless, the lack of the genome-engineering tools for the genus Clostridium is the major hurdle for the economic production of butanol. More recently, genome engineering tools have been developed for metabolic engineering of butanol-producing Clostridium species, which includes genome scale network model and genome editing tools on the basis of mobile group II introns and CRISPR/Cas system. In this study, the genome engineering tools for butanol-producing Clostridium species have been reviewed with a brief future perspective.

• BMB Reports
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• v.38 no.5
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• pp.571-576
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• 2005

Cytokines are proteins produced by many different cells of the immune system and play a significant role in initiating and regulating the inflammatory process. In this research, an important cytokine, interleukin-10 (IL-10) gene, has been identified and characterized from zebrafish (Danio rerio) genome database. Zebrafish IL-10 is located within a 2690 bp fragment and contains five exons and four introns, sharing the same organization with mammalian IL-10 genes. An open reading frame of 543 bp was found to encode a putative 180 amino acid protein with a signal peptide of 22 amino acids, which shares 29.7-80.9% homology with amino acid sequences of other known IL-10. The signature motif of IL-10 is also conserved in zebrafish IL-10. The predicted transcript was finally confirmed by sequencing of cDNA clones. Multi-tissue reverse transcriptase PCR (RT-PCR) was performed to examine the tissue distribution and expression regulation of this gene in seven organs of normal and lipopolysaccharide (LPS) stimulation zebrafish. The results demonstrated that this gene was expressed slightly in normal kidney, gill and gut, no expression was detected in other four tissues. The expression was clearly upregulated after LPS stimulation. Using the ideal zebrafish model, further study of IL-10 characterization and function may provide insight on the understanding of the innate immune system.

• BMB Reports
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• v.39 no.5
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• pp.626-635
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• 2006

Lysophosphatidic acid acyltransferase (LPAAT) is an intrinsic membrane protein that catalyzes the synthesis of phosphatidic acid (PA) from lysophosphatidic acid (LPA). It is well known that LPAAT is involved in lipid biosynthesis, while its role in tumour progression has been of emerging interest in the last few years. To date, seven members of the LPAAT gene family have been found in human. Here we report a novel LPAAT member, designated as LPAAT-theta, which was 2728 base pairs in length and contained an open reading frame (ORF) encoding 434 amino acids. The LPAAT-theta gene consisted of 12 exons and 11 introns, and mapped to chromosome 4q21.23. LPAAT-theta was ubiquitously expressed in 18 human tissues by RT-PCR analysis. Subcellular localization of LPAAT-theta-EGFP fusion protein revealed that LPAAT-theta was distributed primarily in the endoplasmic reticulum (ER) of COS-7 cells. Furthermore, we found that the overexpression of LPAAT-theta can induce mTOR-dependent p70S6K phosphorylation on Thr389 and 4EBP1 phosphorylation on Ser65 in HEK293T cells.

• BMB Reports
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• v.40 no.3
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• pp.325-332
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• 2007

The mitogen-activated protein kinase (MAPK) cascade is one of the major and evolutionally conserved signaling pathways and plays pivotal role in the regulation of stress and developmental signals in plants. Here, a novel gene, termed Gossypium hirsutum MAPK (GhMAPK), was isolated from cotton. The full-length cDNA of GhMAPK encodes for a 372 amino acid protein that contains all 11 of the MAPK conserved subdomains and the phosphorylationactivation motif, TEY. Amino acid sequence alignment revealed that GhMAPK shared high identity with group-C MAPK in plants and showed 83~89% similarities with MAPKs from Arabidopsis, apricot, pea, petunia, and tobacco. Southern blot analysis indicated that the GhMAPK belonged to a multygene family in cotton. Two introns were found within the region of genomic sequence. Northern blot analysis revealed that the transcripts of GhMAPK accumulated markedly when the cotton seedlings were subjected to various abiotic stimuli such as wounding, cold (4$^{\circ}C$), or salinity stress; Furthermore, GhMAPK was upregulated by the exogenous signaling molecules, such as salicylic acid (SA) and hydrogen peroxide ($H_2O_2C$), as well as pathogen attacks. These results indicate that the GhMAPK, which has a high degree of identity with group-C plant MAPKs, may also play an important role in response to environmental stresses.

• Journal of Plant Biotechnology
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• v.7 no.1
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• pp.17-25
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• 2005

We have mined each of the five A. thaliana chromosomes for the presence of simple sequence repeats (SSRs) and developed custom perl scripts to examine their distribution and abundance in relation to genomic position, local G/C content and location within and around transcribed sequences. The distribution of repeats and G/C content with respect to genomic regions (exons, UTRs, introns, intergenic regions and proximity to expressed genes) are shown. SSRs show a non-random distribution across the genome and a strong association within and around transcribed sequences, while G/C density is associated specifically with the coding portions of transcribed sequences. SSR motif repeat number shows a high degree of variation for each SSR type and a high degree of motif sequence bias reflecting local genome sequence composition. PCR primers suitable for the amplification of identified SSRs have been designed where possible, and are available for further studies.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.139-139
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• 2017

The complete chloroplast genome sequence of Avena sterilis L., a dominant wild oat species in the family Poaceae, is first reported in this study. The complete cp genome sequence of A. sterilis is 135,887 bp in length with 38.5% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (21, 603 bp) separated by a small single-copy region (12,575 bp) and a large single-copy region (80,106). The A. sterilis cp genome encodes 111 unique genes, 76 of which are protein-coding genes, 4 rRNA genes, 30 tRNA genes and 18 duplicated genes in the inverted repeat region. Nine genes contain one or two introns. Pair-wise alignments of cp genome were performed for genome-wide comparison. This newly determined cp genome sequence of A. sterilis will provide valuable information for the future breeding programs of valuable cereal crops in the family Poaceae.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.89-89
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• 2017

A gene encoding squalene synthase from grain amaranth was cloned and characterized. The full-length cDNA was 1805-bp long and contained a 1248-bp open reading frame encoding a protein of 416 amino acids with a molecular mass of 47.6 kDa. Southern blot analysis revealed that the A. cruentus genome contained a single copy of the gene. Comparison of the cDNA and genomic sequences indicated that the amaranth SQS gene had 12 introns and 13 exons. All of the exons contributed to the coding sequence. The predicted amino acid sequence of the SQS cDNA shared high homology with those of SQSs from several other plants. It contained conserved six domains that are believed to represent crucial regions of the active site. We conducted qRT-PCR analyses to examine the expression pattern of the SQS gene in seeds at different developmental stages and in several tissues. The amaranth SQS gene was low levels of SQS transcripts at the initial stage of seed development, but the levels increased rapidly at the mid-late developmental stages before declining at the late developmental stage. These findings showed that the amaranth SQS is a late-expressed gene that is rapidly expressed at the mid-late stage of seed development. In addition, we observed that the SQS mRNA levels in stems and roots increased rapidly during the four- to six-leaf stage of development. Therefore, our results showed that the expression levels of SQS in stem and root tissues are significantly higher than those in leaf tissues. In present study provides useful information about the molecular characterization of the SQS clone isolated from grain amaranth. Finally, a basic understanding of these characteristics will contribute to further studies on the amaranth SQS.