• Korean Journal of Microbiology
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• v.41 no.3
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• pp.157-163
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• 2005

The acetate kinase gene from the copepod Paracyclopina nana was cloned. The open reading frame (ORF) was 1,200 bp, and poly(A) signal sequence was located in the end of the ORF. After the molecular phylogenetic analysis of P nana acetate kinase gene, it was revealed that it formed the same branch with that of Aspergillus. Also P. nana acetate kinase showed the difference with those of other prokaryotic microorganisms but showed the same clade with those of fungi. We also confirmed that the recombinant protein of P. nana acetate kinase made approximately 50 kDa after expression of recombinant gene construct in E. coli. This may be useful to compare this protein to those of other organisms in biochemical characteristics.

• The Korean Journal of Mycology
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• v.25 no.1 s.80
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• pp.1-5
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• 1997

The cDNA encoding ${\beta}-tubulin$ of Pleurotus sajor-caju was isolated using an internal gene segment probe amplified by polymerase chain reaction (PCR) of genomic DNA and by cDNA library screening. The cDNA was consisted of 1560 nucleotides(nt), including a 5'-untranslation region (UTR) of 27nt, an open reading frame (ORF) of 1341nt, and a 3'-UTR of 191nt. The ORF encoded a protein of 446 amino acids(aa), which shows over 80% homology with ${\beta}-tubulins$ of other filamentous fungi. Southern hybridization analysis showed that there were two isotypes of ${\beta}-tubulin$ genes in P. sajor-caju. Through sequence analysis we found that ${\beta}-tubulin$ had a unusual $Cys^{165}$ residue, which might be a significant factor for the insensitivity of fungi to fungicide benomyl.

• The Plant Pathology Journal
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• v.27 no.3
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• pp.285-290
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• 2011

Fusarium graminearum virus 2 (FgV2) infects Fusarium graminearum strain 98-8-60 and has at least five segments of double-stranded RNAs (dsRNAs), denoted as dsRNA-1 to dsRNA-5. In this study, the genome of FgV2 was sequenced and its phylogenetic relationship with other mycoviruses was analyzed. The lengths of FgV2 dsRNAs 1-5 ranged from 2414 to 3580 base pairs (bp). The 5' and 3' untranslated regions (UTRs) are highly conserved, and each dsRNA segment had 78-105 and 84-306 bp of 5' and 3' UTRs, respectively. Each dsRNA segment contained a single open reading frame (ORF). Computer analysis of dsRNA-1 revealed a putative open reading frame (ORF) that shows high sequence identity with an RNA-dependent RNA polymerase (RdRp) containing eight conserved motifs. dsRNAs 2-5 also each contain one putative ORF coding for products of unknown function. The sequences of FgV2 dsRNA-2 and dsRNA-3 have significant sequence identity with Magnaporthe oryzae chrysovirus 1 (MoCV1) dsRNA-3 and -4, respectively. When compared to other dsRNA mycoviruses in a phylogenetic analysis of the putative RdRp protein, FgV2 was found to form a distinct virus clade with Aspergillus mycovirus 1816 and MoCV1 in the family Chrysoviridae.

• Journal of Microbiology and Biotechnology
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• v.32 no.9
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• pp.1134-1145
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• 2022

SCO6993 (606 amino acids) in Streptomyces coelicolor belongs to the large ATP-binding regulators of the LuxR family regulators having one DNA-binding motif. Our previous findings predicted that SCO6993 may suppress the production of pigmented antibiotics, actinorhodin, and undecylprodigiosin, in S. coelicolor, resulting in the characterization of its properties at the molecular level. SCO6993-disruptant, S. coelicolor ΔSCO6993 produced excess pigments in R2YE plates as early as the third day of culture and showed 9.0-fold and 1.8-fold increased production of actinorhodin and undecylprodigiosin in R2YE broth, respectively, compared with that by the wild strain and S. coelicolor ΔSCO6993/SCO6993⁺. Real-time polymerase chain reaction analysis showed that the transcription of actA and actII-ORF4 in the actinorhodin biosynthetic gene cluster and that of redD and redQ in the undecylprodigiosin biosynthetic gene cluster were significantly increased by SCO6993-disruptant. Electrophoretic mobility shift assay and DNase footprinting analysis confirmed that SCO6993 protein could bind only to the promoters of pathway-specific transcriptional activator genes, actII-ORF4 and redD, and a specific palindromic sequence is essential for SCO6993 binding. Moreover, SCO6993 bound to two palindromic sequences on its promoter region. These results indicate that SCO6993 suppresses the expression of other biosynthetic genes in the cluster by repressing the transcription of actII-ORF4 and redD and consequently negatively regulating antibiotic production.

• International Journal of Industrial Entomology and Biomaterials
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• v.16 no.2
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• pp.87-92
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• 2008

Bombyx mori nucleopolyhedrovirus (BmNPV) orf47 gene was characterized for the first time. The coding sequence of Bm47 was amplified and subcloned into the prokaryotic expression vector pET-30a(+) in order to produce His-tagged fusion protein in the BL21 (DE3) cells. The His-Bm47 fusion protein was expressed efficiently after induction with IPTG. The purified fusion protein was used to immunize New Zealand white rabbits to prepare polyclonal antibody. As the genome of BmNPV is available in GenBank and the EST database of BmNPV is expanding, identification of novel genes of BmNPV was conceivable by data-mining techniques and bioinformatics tools. Structural bioinformatics approach to analyze the properties of Bm47 encodes protein.

• Journal of Microbiology and Biotechnology
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• v.7 no.4
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• pp.223-228
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• 1997

A DNA fragment containing the gene for cell wall hydrolase of alkalophilic Bacillus subtilis BL-29 was cloned into E. coli JM109 using pUC18 as a vector. A recombinant plasmid, designated pCWL45B, was contained in the fragment originating from the alkalophilic B. subtilis BL-29 chromosomal DNA by Southern hybridization analysis. The nucleotide sequence of a 1.6-kb HindIII fragment containing a cell wall hydrolase-encoding gene was determined. The nucleotide sequence revealed an open reading frame (ORF) of 900 bp with a concensus ribosome-binding site located 6 nucleotide upstream from the ATG start codon. The primary amino acid sequence deduced from the nucleotide sequence revealed a putative protein of 299 amino acid residues with an M.W. of 33, 206. Based on comparison of the amino acid sequence of the ORF with amino acid sequences in the GenBank data, it showed significant homology to the sequence of cell wall amidase of the PBSX bacteriophage of B. subtilis.

• Interdisciplinary Bio Central
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• v.5 no.2
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• pp.5.1-5.3
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• 2013

Introduced were two biological investigations in which information biology played a significant role. In the first case independent findings in cancer research over a long period were united and organized by information biology and led to the outcome that was subject to a Nobel Prize. The outcome has revealed that the cause of human cancer is located in the genome in a dormant condition. The second case shows how to elucidate the function of an unknown DNA sequence or ORF in prokaryotes by a large - scale computer homology search and analyses. For the elucidation the International DNA Databases and a large - scale computer were two key factors.

• Korean Journal of Environmental Biology
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• v.23 no.3 s.59
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• pp.269-274
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• 2005

The 2D/E gel analysis for polypeptide expression reflecting I-18 C gene (early-ecdysterone inducible gene) has conducted the emerged C. riparius adults from larval phase exposure to tebufenozide acting as an ecdysteroidal molting hormone. Control group, the amount of ORE II of the I-18 C gene was larger than that of ORE I of this gene. After treatments, ORE I of the I-18 C gene was overexpressed as the polypeptide, whereas ORF II of this gene was expressed as the polypeptide and was clearly reduced expression. Accordingly, we consider that tebufenozide exhibited endocrine disruptions related processing of ecdysteroid receptor protein reflecting ORF II of I-18 C gene. Also, earlier emergence day was related overexpressed polypeptide reflecting ORE I of I-18 C gene. In this study result, tebufenozide induced changing of physiological condition, and then polypeptide expression reflecting early-ecdysterone inducible I-18 C gene was different between control group and exposure group.

• Journal of the Korean Institute of Intelligent Systems
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• v.18 no.1
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• pp.27-31
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• 2008

많은 바이오인포매틱스 관련 데이터베이스와 도구가 네트워크를 통해서 제공되고 있고, 이들을 효과적으로 활용하면 생물학적 분석을 적은 비용으로 우수한 결과를 얻을 수 있다. 이 논문에서는 주어진 질의에 대해서 잠재적으로 관련된 DNA 서열 정보를 획득하고, 분석자가 관심 있는 항목을 선택하면, 선택된 항목에 대한 모든 DNA 서열 정보를 확보하고, 이들에 대해서 아미노산 서열로 자동변환하여 ORF라는 정보를 활용하여 가장 가능성이 큰 것을 추천하는 도구를 소개한다. 해당 도구에는 웹 로봇 기법과 ORF 검색등을 위한 생물학적 지식을 활용한다.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.12-18
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• 2006

Thirty five Salmonella enterica serovar Typhimurium strains were isolated from diarrheic patients and pigs in Gyeongbuk area from 2003 to 2004. All 35 strains (17 strains from diarrheic patients and 18 from pigs) were resistant to more than one drug and most of strains isolated from pigs were resistant to ampicillin, ohloram-phenicol, streptomycin, sulfamethoxazole-trimethoprime, tetracyclin and nalidixic acid. Each isolate was also screened or the presence of class I, II and III integron gene cassettes. Among 35 strains,3 out of 17 strains isolated from diarrheic patients, carried dhfrX-orfF-aadA2 integron gene cassette and among 18 strains isolated from diseased pigs, 11 strains carried dhfrX-orfF-aadA2 integron gene cassette and 1 strain carried aadA2 integron only. But any class II and class II integron gene cassette were not detected in 35 strains. Thirty five strains were divided by five pulsotypes. Thirty one strains out of thirty five were pulsotype A. Among the remaining 4 strains, one each strain belonged to pulsotype B, C, D and pulsotype E. This data of pulsotypes showed that the widespread of pulsotype A, Salmonella enterica serovar Typhimurium in human and pigs in Gyeongbuk area may have been caused by the dissemination of a few epidemic strains in this area. Thirteen strains contain dhfrX-orfF-aadA2 integron gene cassette showed pulsotype A and one strain contains dhfrX-orfF-aadA2 integron gene cassette showed pulsotype B. One strain contains aadA2 integron showed pulsotype E. But fifteen strains do not contain any integron showed pulsotype A.