• Journal of Microbiology and Biotechnology
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• 제28권2호
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• pp.323-329
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• 2018

In Escherichia coli, the transcription of genes related to metal homeostasis is activated by the presence of target metals. The promoter regions of those genes can be fused with reporter genes to generate whole-cell bioreporters (WCBs); these organisms sense the presence of target metals through reporter gene expression. However, the limited number of available promoters for sensing domains restricts the number of WCB targets. In this study, we have demonstrated an alternative method to generate novel WCBs, based on the notion that since the sensing mechanisms of WCBs are related to metal transportation systems, their properties can be modulated by disrupting metal homeostasis. Mutant E. coli strains were generated by deleting the znt-operon genes zntA, which encodes a zinc-export protein, and zntR, which encodes a znt-operon regulatory protein, to investigate the effects on the metal-sensing properties of WCBs. Deletion of zntA increased the sensitivity but abolished the selectivity of cadmium-sensing WCBs, whereas arsenic-sensing WCBs gained sensitivity toward cadmium. When zntR was deleted, cadmium-sensing WCBs lost the ability to detect cadmium, and this was recovered by introducing exogenous zntR. In addition, the metal-binding site of ZntR was genetically engineered to modulate metal selectivity. This study provides a valuable platform for the development of novel E. coli-based WCBs.

• The Plant Pathology Journal
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• 제29권3호
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• pp.234-241
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• 2013

Polygalacturonase (PG) gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution.

• Genomics & Informatics
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• 제14권3호
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• pp.78-84
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• 2016

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

• Ocean and Polar Research
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• 제44권3호
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• pp.209-220
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• 2022

Carbonic anhydrase (CA) is a key controller of the carbon concentrating mechanism (CCM), and is known to be affected by ambient pH and CO₂ compositions. Herein, we characterized three novel CAs genes (PmCA1, 2, and 3) from the marine dinoflagellate Prorocentrum minimum, and evaluated the relative expressions of the PmCAs and photosynthetic genes PmatpB and PmrbcL under different pH conditions. Each PmCA was predicted to have amino acid residues constituting the zinc binding site. With signal peptide, PmCA1 and PmCA2 were predicted to be intracellular CAs located in the cytoplasm and chloroplast membrane, respectively. On the other hand, PmCA3 was predicted to be extracellular CA located in the plasma membrane. Also, PmCA1 was classified into the beta family, and PmCA2 and PmCA3 were classified into the alpha family via phylogenic analysis. The photosynthesis efficiency of P. minimum was similar at pH 7 to 9, and decreased significantly at pH 6 and pH 10. Overall, relative gene expression levels of the three PmCAs decreased at low pH, and increased as pH increased. Photosynthesis related genes, PmatpB and PmrbcL, showed similar expression patterns to those of PmCAs. These results suggest that changes in seawater pH may affect photosynthesis and CO₂ metabolism in marine dinoflagellates.

• Journal of Microbiology and Biotechnology
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• 제32권10호
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• pp.1262-1274
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• 2022

Cholangiocarcinoma (CCA) is a complex and refractor type of cancer with global prevalence. Several barriers remain in CCA diagnosis, treatment, and prognosis. Therefore, exploring more biomarkers and therapeutic drugs for CCA management is necessary. CCA gene expression data was downloaded from the TCGA and GEO databases. KEGG enrichment, GO analysis, and protein-protein interaction network were used for hub gene identification. miRNA were predicted using Targetscan and validated according to several GEO databases. The relative RNA and miRNA expression levels and prognostic information were obtained from the GEPIA. The candidate drug was screened using pharmacophore-based virtual screening and validated by molecular modeling and through several in vitro studies. 301 differentially expressed genes (DEGs) were screened out. Complement and coagulation cascades-related genes (including AHSG, F2, TTR, and KNG1), and cell cycle-related genes (including CDK1, CCNB1, and KIAA0101) were considered as the hub genes in CCA progression. AHSG, F2, TTR, and KNG1 were found to be significantly decreased and the eight predicted miRNA targeting AHSG, F2, and TTR were increased in CCA patients. CDK1, CCNB1, and KIAA0101 were found to be significantly abundant in CCA patients. In addition, Molport-003-703-800, which is a compound that is derived from pharmacophores-based virtual screening, could directly bind to CDK1 and exhibited anti-tumor activity in cholangiocarcinoma cells. AHSG, F2, TTR, and KNG1 could be novel biomarkers for CCA. Molport-003-703-800 targets CDK1 and work as potential cell cycle inhibitors, thereby having potential for consideration for new chemotherapeutics for CCA.

• Mycobiology
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• 제49권6호
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• pp.582-588
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• 2021

The interaction of mating pheromone and pheromone receptor from the B mating-type locus is the first step in the activation of the mushroom mating signal transduction pathway. The B mating-type locus of Lentinula edodes is composed of Bα and Bβ subloci, each of which contains genes for mating pheromone and pheromone receptor. Allelic variations in both subloci generate multiple B mating-types through which L. edodes maintains genetic diversity. In addition to the B mating-type locus, our genomic sequence analysis revealed the presence of a novel chromosomal locus 43.3 kb away from the B mating-type locus, containing genes for a pair of mating pheromones (PHBN1 and PHBN2) and a pheromone receptor (RCBN). The new locus (Bα-N) was homologous to the Bα sublocus, but unlike the multiallelic Bα sublocus, it was highly conserved across the wild and cultivated strains. The interactions of RcbN with various mating pheromones from the B and Bα-N mating-type loci were investigated using yeast model that replaced endogenous yeast mating pheromone receptor STE2 with RCBN. The yeast mating signal transduction pathway was only activated in the presence of PHBN1 or PHBN2 in the RcbN producing yeast, indicating that RcbN interacts with self-pheromones (PHBN1 and PHBN2), not with pheromones from the B mating-type locus. The biological function of the Bα-N locus was suggested to control the expression of A mating-type genes, as evidenced by the increased expression of two A-genes HD1 and HD2 upon the treatment of synthetic PHBN1 and PHBN2 peptides to the monokaryotic strain of L. edodes.

• 한국정보통신학회:학술대회논문집
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• 한국정보통신학회 2012년도 추계학술대회
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• pp.994-996
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• 2012

본 연구실에서는 새로운 베큘로바이러스 벡터 시스템을 구축하였다. 즉 본 벡터 시스템은 polyhedron promoter, vesicular stomatitis virus G (VSVG), polyA, cytomegalovirus (CMV) promoter, enhanced green fluorescent protein (EGFP), protein transduction domain (PTD)을 코딩하는 유전자들로 구성 되어있다. 이렇게 새로이 제작된 베큘로바이러스 벡터 시스템과 대조군의 벡터 시스템과 효율과 발현율을 비교하였다. 그 결과 본 연구실에서 제작된 베큘로바이러스 벡터 시스템이 다른 대조군의 벡터 시스템에 비해 효과적임을 확인할 수 있었다.

• 식품과학과 산업
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• 제52권2호
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• pp.171-187
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• 2019

Novel food materials can be produced based on biotechnology such as genetic recombination, microbial fermentation, and enzymatic engineering by utilizing living organisms such as animal, plant, and microorganism or by applying the enzymes isolated from them. Especially, exploration and development of novel prebiotics and probiotics attracted great attention worldwide in the food industry, of which the research and industrial trends in food biotechnology field are promoting the production of next generation sweeteners and proliferation of beneficial bacteria in gastrointestinal tract. Development and commercialization of novel food materials by domestic bioprocessing technology have been sluggish due to the GMO/LMO food safety issues. Meanwhile, the US and EU do not perceive badly about gene manipulation technology, and the research is most active in the fields of crops and GMMs, respectively. Genetic scissors, which are considered as next generation technology, are notable since foreign genes do not remain in final products.

• 한국양식학회:학술대회논문집
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• 한국양식학회 2003년도 추계학술발표대회 논문요약집
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• pp.43-43
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• 2003

EST analysis was performed to identify stress-responsive and immune-related genes from rock bream (Oplegnathus fasciatus). cDNA libraries were constructed with liver and randomly chosen 624 clones were subjected to automated sequence analysis. Of 624 clones sequenced in total, approximately 15% of ESTs was novel sequences (no match to GenBank) or sequences with high homology to hypothetical/unknown genes. The bioinforamtic sequence analysis including functional clustering, homology grouping, contig assembly with electronic northern and organism matches were carried out. Several potential stress-responsive biomarker and/or immune-related genes were identified in all the tissues examined. It included lectins, ferritins, CP450, proteinase, proteinase inhibitors, anti-oxidant enzymes, various heat-shock proteins, warm temperature acclimation protein, complements, methyltransferase, zinc finger proteins, lysozymes, macrophage maturation associated protein, and others. This information will offer new possibilities as fundamental baseline data for understanding and addressing their molecular mechanism involved in host defense and immune systems of this species.

• 대한의생명과학회지
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• 제21권2호
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• pp.60-68
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• 2015

NecroX-7 is a novel small compound of the NecroX series based on the indole moiety, which has potent cytoprotective and antioxidant properties. We previously detected potential immune regulatory effects of NecroX-7 in immune related diseases like Graft-versus-Host Disease. However, the function and the underlying mechanisms of immunological effects of NecroX-7 in the immune system have not been well established. In this study, we investigated the immune response characterization of differentially expressed genes of NecroX-7 administration in $CD4^+$ T cells by microarray analysis. $CD4^+$ T cells stimulated with NecroX-7 ($40{\mu}M$) or vehicle for 72 hours resulted in the identification of 337 differentially expressed genes (1.5 fold, P<0.05) by expression profiling analysis. Twenty eight of the explored NecroX-7-regulated genes were related to immune system processes. These genes were validated by quantitative real-time PCR. The most significant genes were glutathione reductase, eukaryotic translation elongation factor 1, lymphotoxin-alpha, heat shock protein 9 and chloride intracellular channel protein 4. These findings demonstrate the strongly immune response of NecroX-7 in $CD4^+$ T cells, suggesting that cytoprotection and immune regulation may underlie the critical aspects of NecroX-7 exposure.