• Korean Journal of Ecology and Environment
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• v.38 no.4 s.114
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• pp.510-517
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• 2005

The filamentous cyanobacterium Anabaena is capable of both photosynthesis and nitrogen fixation which probably facilitated its incredible adaptation and proliferation in freshwater environments. A small gene, patS, was found to block nitrogen fixing cells from developing which resulted in death of Anabaena in the absence of combined nitrogen sources. We analyzed the DNA sequences in the vicinity of the patS gene by using a codon usage program and detected no codon bias other than the patS open reading frame. Three overlapping cosmids that contain the patS gene were identified, and the presence of other known heterocyst-controlling genes was examined. The patS expression in response to nitrogen starvation was analyzed at the level of transcription and translation by using Northern blot analyses and lacZ-reporter-gene fusion experiments, respectively. The patS expression increased rapidly (within 12 hours) upon the removal of combined nitrogen from the media.

• Proceedings of the Korea Contents Association Conference
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• 2007.11a
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• pp.522-526
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• 2007

Since newly emerged disease, the Severe Acute Respiratory Syndrome (SARS), spread from Asia to North America and Europe rapidly in 2003, many researchers have tried to determine where the virus came from. In the phylogenetic point of view, SARS virus has been known to be one of the genus Coronavirus, but, the overall conservation of SARS virus sequence was not highly similar to that of known coronaviruses. The natural reservoirs of SARS-CoV are not clearly determined, yet. In the present study, the genomic sequences of SARS-CoV were analyzed by bioinformatics techniques such as multiple sequence alignment and phylogenetic analysis methods as well multivariate statistical analysis. All the calculating processes, including calculations of the relative synonymous codon usage (RSCU) and other genomic parameters using 30,305 coding sequences from the two genera, Coronavirus, and Lentivirus, and one family, Orthomyxoviridae, were performed on SMP cluster in KISTI, Supercomputing Center. As a result, SARS_CoV showed very similar RSCU patterns with feline coronavirus on the both axes of the correspondence analysis, and this result showed more agreeable results with serological results for SARS_CoV than that of phylogenetic result itself. In addition, SARS_CoV, human immunodeficiency virus, and influenza A virus commonly showed the very low RSCU differences among each synonymous codon group, and this low RSCU bias might provide some advantages for them to be transmitted from other species into human beings more successfully. Large-scale genomic analysis using bioinformatics techniques may be useful in genetic epidemiology field effectively.

• Microbiology and Biotechnology Letters
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• v.49 no.1
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• pp.75-87
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• 2021

Type I Interferons (IFNα) are known for their role as biological anticancer agents owing to their cell-apoptosis inducing properties. Development of an appropriate, cost-effective host expression system is crucial for meeting the increasing demand for proteins. Therefore, this study aims to develop codon-optimized IFNα-2b in L. lactis NZ3900. These cells express extracellular protein using the NICE system and Usp₄₅ signal peptide. To validate the mature form of the expressed protein, the recombinant IFNα-2b was screened in a human colorectal cancer cell line using the cytotoxicity assay. The IFNα-2b was successfully cloned into the pNZ8148 vector, thereby generating recombinant L. lactis pNZ8148-SP_Usp45-IFNα-2b. The computational analysis of codon-optimized IFNα-2b revealed no mutation and amino acid changes; additionally, the codon-optimized IFNα-2b showed 100% similarity with native human IFNα-2b, in the BLAST analysis. The partial size exclusion chromatography (SEC) of extracellular protein yielded a 19 kDa protein, which was further confirmed by its positive binding to anti-IFNα-2b in the western blot analysis. The crude protein and SEC-purified partial fraction showed IC₅₀ values of 33.22 ㎍/ml and 127.2 ㎍/ml, respectively, which indicated better activity than the metabolites of L. lactis NZ3900 (231.8 ㎍/ml). These values were also comparable with those of the regular anticancer drug tamoxifen (105.5 ㎍/ml). These results demonstrated L. lactis as a promising host system that functions by utilizing the pNZ8148 NICE system. Meanwhile, codon-optimized usage of the inserted gene increased the optimal protein expression levels, which could be beneficial for its large-scale production. Taken together, the recombinant L. lactis IFNα-2b is a potential alternative treatment for colorectal cancer. Furthermore, its activity was analyzed in the WiDr cell line, to assess its colorectal anticancer activities in vivo.

• Microbiology and Biotechnology Letters
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• v.23 no.2
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• pp.138-144
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• 1995

The cDNA, encoding human lysozyme (HLY) which was isolated from a human placenta cDNA library, has been well characterized (Yoshimura et al., 1988). Based on the communication, we have prepared an artificial HLY gene from chemically synthesized 38-oligomer with high codon usage in Saccharomyces cerevisiae. For directing the synthesis and secretion of HLY in S. cerevisiae, an expression vector, pHKl was constructed by inserting the HLY gene, containing a synthetic HLY secretion signal sequence, between the yeast GAP promoter and PH05 terminator. From a lysoplate assay, we have confirmed an yeast transformant harboring a pHK1 which makes a clearing zone on the overlayed Micrococcus luteus. This result means a chemically synthesized HLY gene which was normally expressed and secreted in yeast.

• Journal of Microbiology and Biotechnology
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• v.22 no.9
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• pp.1202-1207
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• 2012

A gene, ClCDA, encoding chitin deacetylase from Colletotrichum lindemuthianum, was optimized according to the codon usage bias of Pichia pastoris and synthesized in vitro by overlap extension PCR. It was secretorily expressed in P. pastoris GS115 using the constitutive expression vector pHMB905A. The expression level reached the highest with 110 mg/l culture supernatant after 72 h of methanol induction, which comprised 77.27 U/mg chitin deacetylase activity. SDS-PAGE, mass spectrometry, and deglycosylation assays demonstrated that partial recombinant protein was glycosylated with an apparent molecular mass of 33 kDa. The amino acid sequences of recombinant proteins were confirmed by mass spectrometry.

• Animal Systematics, Evolution and Diversity
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• v.26 no.3
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• pp.197-201
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• 2010

We sequenced the whole mitochondrial genome of Dendronephthya gigantea (Anthozoa: Octocorallia: Nephteidae), the first mitochondrial genome sequence report in the Family Nephtheidae. The mitochondrial genome of D. gigantea was 18,842 bp in length, and contained 14 protein coding genes (atp6 and 8, cox1-3, cytb, nd1-6 and 4L, and msh1), two ribosomal RNAs, and only one transfer RNA. The gene content and gene order is identical to other octocorals sequenced to date. The portion of the noncoding regions is slightly larger than the other octocorals (5.08% compared to average 3.98%). We expect that the information of gene content, gene order, codon usage, noncoding region and protein coding gene sequence could be used in the further analysis of anthozoan phylogeny.

• BMB Reports
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• v.41 no.5
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• pp.404-407
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• 2008

A 345-bp gene that encodes human bone morphogenetic protein-2 (hBMP-2) has been synthesized. The codon usage of the resulting gene was modified to include those triplets that are utilized in highly expressed Escherichia coli genes. The hBMP-2 gene was efficiently expressed in E. coli as a soluble and active protein. Since the recombinant hBMP-2 was readily solublized, no further solublization steps were required throughout purification. No additional tagging residues were introduced into the synthetic hBMP-2 gene product. The developed synthetic gene is a promising approach for scaling-up the soluble expression of hBMP-2.

• Microbiology and Biotechnology Letters
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• v.22 no.5
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• pp.477-484
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• 1994

Using a methylotrophic yeast Hansenula polymorpha, a heterologous gene expression and secretion system was developed for the production of hEGF(human Epidermal Growth Factor) which has been shown to promote epithelial cell proliferation and to inhibit gastric acid secretion. The hEGF gene was chemically synthesized according to the preferred codon usage in H. polymor- pha and expressed under the control of the strong and inducible methanol oxidase(MOX) promoter. The mating factor $\alpha$ pre-pro leader sequence of Saccharomyces cerevisiae was employed for hEGF to be secreted into the extracellular medium. This expression cassette was stably integrated into the host chromosomal DNA. Mature hEGF was efficiently expressed and secreted into the extracel- lular medium. About 24 mg/l of hEGF was detected in the cuture supernatant of a transformant with pA-EGF3 under the suboptimal culture conditions.

• Molecules and Cells
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• v.28 no.3
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• pp.155-165
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• 2009

The newly sequenced complete mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys($St{\aa}l$) (Hemiptera: Pentatomidae), is a circular molecule of 16,518 bp with a total A+T content of 76.4% and two extensive repeat regions in A+T rich region. Nucleotide composition and codon usage of H. halys are about average when compared with values observed in 19 other published hemipteran mitochondrial genomes. Phylogenetic analyses using these 20 hemipteran mitochondrial genomes support the currently accepted hypothesis that suborders Heteroptera and Auchenorrhyncha form a monophyletic group. The mitochondrial gene arrangements of the 20 genomes are also consistent with our results.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.210-219
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• 2003

오페론(operon)은 보통 미생물에서 다수의 인접한 유전자들로 구성된 그룹으로 하나의 유전자처럼 공통된 프로모터에 의해 전사되는 단위이다. 오페론을 구성하는 유전자들은 기능적으로 서로 유사하거나 같은 물질대사경로(metabolic pathway) 상에 존재하는 특징을 지니기 때문에 이들은 중요한 의미를 가지며, 미생물 유전체 분석에서 오페론을 구성하는 유전자들을 예측하는 것은 상당히 중요하다. 오페론을 예측하는 이전 연구들로는 이미 알려진 오페론의 특징인 유전자간 거리나 오페론을 구성하는 평균 유전자 개수 등을 이용하는 방법, 마이크로어레이 발현 실험을 이용한 방법, 전유전체(whole genome)들 간의 보존된 유전자 집합(conserved gene cluster)을 이용한 방법 그리고 물질대사경로를 이용한 방법 등이 있다. 본 논문에서는 COG 기능(function) 거리, 유전자 간의 거리, 코돈 사용빈도(codon usage) 그리고COG 기능 거리와 유전자간 거리를 같이 적용한 방법을 이용하여 오페론 예측을 위한 전처리 모델을 생성하였다 전처리 모델을 E. coli 전유전체에 적용해본 결과, 알려진 오페론들의 약 90%가 이를 포함하였다. 따라서 본 논문에서 제시한 전처리 모델은, 추후 오페론 예측을 위한 좋은 도구로 활용할 수 있을 것이다.