• Journal of Microbiology and Biotechnology
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• 제8권3호
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• pp.214-221
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• 1998

A Brevibacterium ammoniagenes gene coding for glucose/mannose-specific enzyme II ($EII^{Glc}$) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS) was cloned by complementing an Escherichia coli mutation affecting a ptsG gene, and the complete DNA nucleotide sequence was determined. The cloned gene was identified to be a ptsG, which enables the E. coli transportment to use glucose more efficiently than mannose as the sole carbon source in an M9 minimal medium. The ptsG gene of B. ammoniagenes consists of an open reading frame of 1,983 nucleotides putatively encoding a polypeptide of 661 amino acid residues and a TAA stop codon. The deduced amino acid sequence of the B. ammoniagenes $EII^{Glc}$ shows, at $46\%$, the highest degree of sequence similarity with the Corynebacterium glutamicum EII specific for both glucose and mannose. In addition, the $EII^{Glc}$ shares approximately $30\%$ sequence similarities with sucrose-specific and ${\beta}$-glucoside-specific EIIs of the several bacteria belonging to the glucose-PTS class. The 161-amino-acid C-terminal sequence of $EII^{Glc}$ is also similar to that of E. coli enzyme $IIA^{Glc}$, specific for glucose ($EIIA^{Glc}$). The B. ammoniagenes $EII^{Glc}$ consists of three domains; a hydrophobic region (EIIC) and two hydrophilic regions (EIIA, EIIB). The arrangement of structural domains, IIBCA, of the $EII^{Glc}$ is identical to those of EIIs specific for sucrose or ${\beta}$-glucoside. While the domain IIA was removed from the B. ammoniagenes $EII^{Glc}$ the remaining domains IIBC were found to restore the glucose and mannose-utilizing capacity of E. coli mutant lacking $EII^{Glc}$ activity with $EIIA^{Glc}$ of the E. coli mutant. $EII^{Glc}$ contains a histidine residue and a cysteine residue which are putative phosphorylation sites for the protein.

• Journal of Microbiology and Biotechnology
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• 제7권2호
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• pp.157-159
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• 1997

A 340-bp chitin synthase gene(CHS) fragment was cloned from the genomic DNA of Pyricularia oryzae using a PCR process with two primer DNAs corresponding to highly conserved sequences within fungal CHS genes. The entire DNA nucleotide sequences of the cloned DNA fragment were determined and analyzed. The amino acid sequences deduced from the nucleotide sequence of the amplified DNA fragment showed 86% homology to that of the Aspergillus fumigatus CHSE gene (9). Using this PCR-amplified DNA, about 2.3 kb of including the PCR fragment of CHSE gene was cloned from genomic library.

• Fisheries and Aquatic Sciences
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• 제13권4호
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• pp.272-277
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• 2010

Seagrasses are marine angiosperms of ecological importance in providing shelter and food to aquatic species as well as maintaining the carbon cycle on earth. Phyllospadix iwatensis is a seagrass of the family Zosteraceae and is distributed along the eastern coast of Korea. The nucleotide sequences of P. iwatensis nuclear genes encoding 18S ribosomal RNA (rRNA) and internal transcribed spacer-1 (ITS-1) were determined for molecular phylogenetic analysis. Genomic DNA was isolated from P. iwatensis and used for PCR amplification of 18S rRNA and ITS-1. Examination of the 18S rRNA sequence of P. iwatensis showed a close (99% similarity) relationship to Zostera noltii, another genus of Zosteraceae, but a distant (84% similarity) evolutionary relationship to other macroalgal Laminariales species. Further discrepancies found in ITS-1 nucleotide sequences between closely related species indicate that the sequence information could be used for species identification.

• 한국연초학회지
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• 제18권2호
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• pp.101-106
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• 1996

Tobacco mosaic virus (TMV) tomato strain was isolated from tomato "Seo-Kwang" in Korea. The virion was purified by density gradient centrifugation, and total viral RNA was isolated from the purified particles. Coat protein (CP) cDNA of the virus was synthesized by RT-PCR, and the purified cDNA fragment was subcloned to pBluescript II SK-. The analysis of nucleotide sequence showed that this cDNA was 693 nucleotides long from the insert of clone p1571 and p1572 which contain complete codons of the viral coat protein gene (474 nucleotides) and 3' untranslated region. The nucleotides of coat protein encoding cDNA of the strain were 6 nucleotides less than that of TMV common strain isolated from tobacco plant in Korea. The CP gene showed 70% maximum homology with that of the common strain in the nucleotide level and 86% maximum homology in amino acid level.cid level.

• 한국미생물·생명공학회지
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• 제24권4호
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• pp.423-426
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• 1996

The complete nucleotide sequence of pKH6, a tetracycline-resistance (Tc$^{r}$) plasmid isolated from multi-drug resistant Staphylococcus aureus SA2, has been determined and compared with that of the staphylococcal Tc$^{r}$ plasmid pTl8l. The nucleotide sequences of the two plasmids are in agreement except for 7 nucleotides. All differences are caused by base pair substitutions. Among 6 substitutions, 3 occurred in coding regions. However, only two base substitutions in coding regions resulted in changes of amino acid sequences in two different ORFs of repC and Pre proteins.

• 약학회지
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• 제39권6호
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• pp.676-680
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• 1995

The nucleotide sequence of Xbal-Mbol fragment of pKH7, a chloramphenicol-resistant($Cm^{r}$) plasmid isolated from multidrug-resistant S. aureus SA2, has been determined. Xbal-Mbol fragment of pKH7 was found to contain two ORFs. One ORF encoded Rap and the other encoded CAT protein. The deduced amino acid sequences of Rep and CAT of pKH7 were compared to those of pUB112 and pC221. Comparisons revealed that there was one amino acid difference in CAT between pKH7 and pUB112. CAT of pKH7 exhibited 98.6% amino acid identity to that of pC221. In case of Rep proteins, a slightly lower homology of 96.4% and 86.7% in amino acid sequences was observed between pKH7 and pUB112 and between pKH7 and pC221, respectively.

• Genomics & Informatics
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• 제18권4호
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• pp.41.1-41.8
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• 2020

We provide an algorithm for the construction and analysis of autocorrelation (information) functions of gene nucleotide sequences. As a measure of correlation between discrete random variables, we use normalized mutual information. The information functions are indicative of the degree of structuredness of gene sequences. We construct the information functions for selected gene sequences. We find a significant difference between information functions of genes of different types. We hypothesize that the features of information functions of gene nucleotide sequences are related to phenotypes of these genes.

• 한국해양생명과학회지
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• 제6권1호
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• pp.38-46
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• 2021

꼬막 종류 중 하나인 Tegillarca granosa는 해양 이매패류로서 한국, 중국, 일본 등의 중요한 수산 자원 중 하나이다. 꼬막의 염색체 수는 2n=38로 알려져 있지만, 유전체의 크기와 유전 정보에 대해서는 아직 명확하게 알려져 있지 않다. 꼬막의 유전체 크기 예측을 위하여 NGS Illumina HiSeq 플랫폼을 이용하여 얻은 짧은 DNA 서열 정보를 통하여 in silico 분석으로 유전체 크기를 분석하였다. 그 결과 꼬막의 유전체 크기는 770.61 Mb로 예측되었다. 이후 MaSuRCA assembler를 통하여 드래프트 게놈 조립 작업을 수행하고, QDD pipeline을 이용하여 SSR (simple sequence repeats) 분석을 수행하였다. 꼬막의 유전체로부터 43,944개의 SSR을 발굴하였으며, 다이-뉴클레오타이드(di-nucleotide) 69.51%, 트라이-뉴클레오타이드(tri-nucleotide) 16.68%, 테트라-뉴클레오타이드(tetra-nucleotide) 12.96%, 펜타-뉴클레오타이드(penta-nucleotide) 0.82% 그리고 헥사-뉴클레오타이드(hexa-nucleotide) 0.03%로 구성되었다. 이후 꼬막의 유전적 다양성 연구에 활용할 수 있는 100개의 마이크로새틀라이트 마커의 프라이머 세트를 선별하였다. 앞으로 이번 연구를 통해서, 꼬막의 집단유전학적 연구와 유전적 다양성을 규명하는데 도움이 될 것이며, 나아가 동종들 간의 원산지 분류를 알아낼 수 있을 것이다.

• 한국미생물·생명공학회지
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• 제22권2호
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• pp.134-142
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• 1994

The neucleotide sequences of the xylA gene encoding $\beta $-xylosidase of Bacillus stearothermophilus and is its flanking regions were datermined. Three open reading frame(ORFs) were found, one of which(ORF1) appeared to code for the $\beta $-xylosidase. The 1830 base pair ORF1 encoded 609 amino acids starting from a TTG initiation codon. The molecular weight deduced from the nucleotide sequence(68 KD) was in agreement with that estimated by SDS-polyacrylamide gel electrophoresis of the purified enzyme(66 KD). The Shine-Dalgarno sequence(5'-AGGAGG-3') was found 11 bp upstream of the initiation codon. Further 15 bp upstream, there observed a potential transcription initiation signals. The putative -10 sequence(CATAAT) and -35 sequence(TTGTTA) coresponded closely to the consensus sequences for Bacillus subtilis RNA polymerase with major sigma factor. The guanine-plus-cytosine content of the coding region of the xylA gene was 56mol% while that of the third position of the codons was 63 mol%. Based on the comparison with the amino acid sequences of several other carbohydrate degrading enzymes, two conserved regions, possibly participating in the catalytic mechamism of $\beta $-xylosidase xylA, were identified in 278-298 and 329-350 regions of the translated xylA gene. The nucleotide sequence of the xylA was found to exhibit no homology to any other genes so far reproted.

• The Plant Pathology Journal
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• 제28권4호
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• pp.428-432
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• 2012

We determined the complete genome sequence of a Vietnamese isolate of Southern rice black-streaked dwarf virus (SRBSDV). Whole genome comparisons and phylogenetic analysis showed that the genome of the Vietnamese isolate shared high nucleotide sequence identities of over 97.5% with those of the reported Chinese isolates, confirming a common origin of them. Moreover, the greatest divergence between different SRBSDV isolates was found in the segments S1, S3, S4 and S6, which differs from the sequence alignment results between SRBSDV and Rice black streaked dwarf virus (RBSDV), implying that SRBSDV evolved in a unique way independent of RBSDV. This is the first report of a complete nucleotide sequence of SRBSDV from Vietnam and our data provides new clues for further understanding of molecular variation and epidemiology of SRBSDV in Southeast Asia.