• 한국연초학회지
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• 제37권1호
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• pp.25-33
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• 2015

Genome walking is a par ticular application for identifying sequences of unknown genomic regions adjacent to a known region. Many genome walking methods based on polymerase chain reaction (PCR) are available. Even if earlier techniques suffer from low reproducibility, inefficiency, and non-specificity, improved strategies have been developed. In this study, we present an alternative strategy: the genomic DNA is digested with restriction enzymes. After cytosine overhangs at 5' ends, the fragments are ligated to linker adaptor s had guanine overhang at 3' ends. Then nested PCR is performed. The improvements in this strategy focus on two points. The first is the C tailing method using Pfu polymerase instead of the A tailing method based on nontemplate-dependent terminal transferase activity of Taq polymerase. Therefore unintended modification of target DNA can be prevented without A tailing error. The second point is the use of C/G-specific ligation had advantage in the ligation efficiency compared with A/T-specific ligation. Therefore, the C-G linker PCR method increases ligation efficiency between digested genomic DNA and adaptor DNA. As a result, the quantity of target DNA to amplify by PCR is enriched. We successfully used G-C linker PCR to retrieve flanking regions bordering the phophinothricin resistance gene in genetically modified tobacco (GMO).

• Horticulture, Environment, and Biotechnology : HEB
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• 제59권6호
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• pp.857-864
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• 2018

Previous studies have not detected transcripts of the gene encoding anthocyanidin synthase (ANS) in white pomegranates (Punica granatum L.) and suggest that a large-sized insertion in the coding region of the ANS gene might be the causal mutation. To elucidate the identity of the putative insertion, 3887-bp 5' and 3392-bp 3' partial sequences of the insertion site were obtained by genome walking and a gene coding for an expansin-like protein was identified in these genome-walked sequences. An identical protein (GenBank accession OWM71963) isolated from pomegranate was identified from BLAST search. Based on information of OWM71963, a 5.8-Mb scaffold sequence with genes coding for the expansin-like protein and ANS were identified. The scaffold sequence assembled from a red pomegranate cultivar also contained all genome-walked sequences. Analysis of positions and orientations of these genes and genome-walked sequences revealed that the 27,786-bp region, including the 88-bp 5' partial sequences of the ANS gene, might be translocated into an approximately 22-kb upstream region in an inverted orientation. Borders of the translocated region were confirmed by PCR amplification and sequencing. Based on the translocation mutation, a simple PCR codominant marker was developed for efficient genotyping of the ANS gene. This molecular marker could serve as a useful tool for selecting desirable plants at young seedling stages in pomegranate breeding programs.

• Journal of Microbiology and Biotechnology
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• 제24권10호
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• pp.1389-1396
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• 2014

The entire nucleotide sequence of the TKL1 gene encoding transketolase (TKL) in an erythritol-producing yeast of Candida magnoliae was determined by degenerate polymerase chain reaction and genome walking. Sequence analysis revealed an open reading frame of C. magnoliae TKL1 (CmTKL1) that spans 2,088 bp and encodes 696 amino acids, sharing 61.7% amino acid identity to Kluyveromyces lactis TKL. Functional analysis showed that CmTKL1 complemented a Saccharomyces cerevisiae tkl1 tkl2 double mutant for growth in the absence of aromatic amino acids and restored transketolase activity in this mutant. An enzyme activity assay and RT-PCR revealed that the expression of CmTKL1 is induced by fructose, $H_2O_2$, and KCl. The GenBank accession number for C. magnoliae TKL1 is KF751756.

• 생명과학회지
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• 제32권8호
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• pp.659-665
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• 2022

Chlorella vulgaris는 인간과 동물에서 주요한 식품의 원료로 이용되는 수 조류이다. 최근 클로렐라는 어류 양식, 생물연료 및 영양물질과 치료용 단백질의 생산을 위한 이용 가능성과 관련하여 많은 관심을 받고 있다. 최근 본 연구실에서는 빠른 성장, 배양의 용이성, 암 조건에서의 배양성을 특징으로 하는 새로운 C. vulgaris PKVL7422균주를 분리하였으나, 이 균주의 질소 이용에 관련된 유전자에 대하여는 보고된 바가 없다. 본 연구에서는 cDNA 말단의 신속 증폭과 genome walking을 이용하여 C. vulgaris PKVL7422의 질산환원 효소(nitrate reductase, NR)를 동정하였다. C. vulgaris PKVL7422 NR 유전자는 약 8 kb이며, 18개의 인트론과 877개의 아미노산을 암호화 하는 19개의 엑손으로 되어 있다. 기존의 알려진 NR 단백질과의 비교 분석 결과 C. vulgaris PKVL7422 NR 단백질은 식물의 NR에 존재하는 5개의 도메인과 다수의 비변이성 아미노산 잔기를 가지고 있는 것으로 확인되었으며, 이러한 결과는 조류 NR 유전자의 분자생물학적 구조에 대한 새로운 정보를 제공한다.

• Journal of Microbiology and Biotechnology
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• 제23권7호
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• pp.984-992
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• 2013

The entire nucleotide sequence of the xylose reductase (XR) gene in Candida milleri CBS8195 sourdough yeast was determined by degenerate polymerase chain reaction (PCR) and genome walking. The sequence analysis revealed an open-reading frame of 981 bp that encoded 326 amino acids with a predicted molecular mass of 36.7 kDa. The deduced amino acid sequence of XR of C. milleri was 64.7% homologous to that of Kluyveromyces lactis. The cloned XR gene was expressed in Saccharomyces cerevisiae, and the resulting recombinant S. cerevisiae strain produced xylitol from xylose, indicating that the C. milleri XR introduced into S. cerevisiae is functional. An enzymatic activity assay and semiquantitative reverse transcription-PCR revealed that the expression of CmXR was induced by xylose. The GenBank Accession No. for CmXR is KC599203.

• Journal of Plant Biotechnology
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• 제35권2호
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• pp.101-108
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• 2008

아그로박테리움을 이용한 형질전환은 대다수의 쌍자엽과 몇몇 단자엽 식물의 게놈내로 외래유전자를 도입하는 성공적인 방법이다. 해충저항성 CryIAc 유전자가 도입된 배추형 질전환체를 아그로박테리움 형질전환법을 통해 얻은 후, 도입유전자의 수를 Southern 분석을 통하여 확인하였다. 배추형질전환체 46개 중에서 29개는 1 copy의 CryIAc 유전자가 도입된 것으로 확인되었다. 식물체의 게놈내로 T-DNA 결합에 관한 정보를 얻기 위해서 LB 인접서열을 genome walking PCR 방법을 통하여 분석하였다. 46개의 배추형질전환체중에서 37개는 운반체의 backbone 염기서열을 지니는 것으로 확인되었다. 이러한 결과는 도입 운반체의 LB 지점에서 제대로 종결이 이루어지지 않아서 운반체의 backbone 염기서열이 운반된 것으로 보여진다. 운반체의 backbone 염기서열이 도입되지 않은 9개체의 배추형질전환체를 LB 인접서열을 분석한 결과, 모든 LB 부위는 절단부위가 보존되지 않았고, 절단부위에서 36bp까지도 결실이 확인되었다.

• 원예과학기술지
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• 제31권1호
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• pp.72-79
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• 2013

Inactivation of the gene coding for dihydroflavonol 4-reductase (DFR) is responsible for the color difference between red and yellow onions (Allium cepa L.). Two inactive DFR-A alleles, DFR-$A^{PS}$ and DFR-$A^{DEL}$, were identified in our previous study. A functional marker was developed on the basis of the premature stop codon that inactivated the DFR-$A^{PS}$ allele. A derived cleaved amplified polymorphic sequences (dCAPS) primer was designed to detect the single nucleotide polymorphism, an A/T transition, which produced the premature stop codon. Digested PCR products clearly distinguished the homozygous and heterozygous red $F_2$ individuals. Meanwhile, to develop a molecular marker for detection of the DFR-$A^{DEL}$ allele in which entire DFR-A gene was deleted, genome walking was performed and approximately 3 kb 5' and 3' flanking sequences of the DFR-$A^R$ coding region were obtained. PCR amplification using multiple primers binding to the extended flanking regions showed that more of the extended region of the DFR-A gene was deleted in the DFR-$A^{DEL}$ allele. A dominant simple PCR marker was developed to identify the DFR-$A^{DEL}$ allele using the dissimilar 3' flanking sequences of the DFR-A gene and homologous DFR-B pseudogene. Distribution of the DFR-$A^{PS}$ and DFR-$A^{DEL}$ alleles in yellow onion cultivars bred in Korea and Japan was surveyed using molecular makers developed in this study. Results showed predominant existence of the DFR-$A^{PS}$ allele in yellow onion cultivars.

• Asian-Australasian Journal of Animal Sciences
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• 제14권6호
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Journal of Microbiology and Biotechnology
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• 제25권8호
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• pp.1324-1327
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• 2015

The nucleotide sequence of the TRP1 gene encoding phosphoribosyl anthranilate isomerase in yeast Saccharomycopsis fibuligera was determined by degenerate polymerase chain reaction and genome walking. Sequence analysis revealed the presence of an uninterrupted open-reading frame of 759 bp, including the stop codon, encoding a 252 amino acid residue. The deduced amino acid sequence of Trp1 in S. fibuligera was 43.5% homologous to that of Komagataella pastoris. The cloned TRP1 gene (SfTRP1) complemented the trp1 mutation in Saccharomyces cerevisiae, suggesting that it encodes a functional TRP1 in S. fibuligera. A new auxotrophic marker to engineer starch-degrading yeast S. fibuligera is now available. The GenBank Accession No. for SfTRP1 is KR078268.

• Journal of Microbiology and Biotechnology
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• 제25권11호
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• pp.1880-1893
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• 2015

In this study, Pseudomonas R0-14, which was isolated from Arctic soil samples, showed a clear halo when grown on M9 medium agarose plates containing olive oil-rhodamine B as substrate, suggesting that it expressed putative lipase(s). A putative lipase gene, lipR, was cloned from R0-14 by genome walking and Touchdown PCR. lipR encodes a 562-amino-acid polypeptide showing a typical α/β hydrolase structure with a catalytic triad consisting of Ser₁₅₃-Asp₂₀₂-His₂₆₀ and one α-helical lid (residues 103-113). A phylogenetic analysis revealed that LipR belongs to the lipase subfamily I.3. LipR was successfully expressed in Escherichia coli, purified, and biochemically characterized. Recombinant LipR exhibited its maximum activity towards p-nitrophenyl butyrate at pH 8.5 and 60℃ with a K_m of 0.37 mM and a k_cat of 6.42 s^-1. It retained over 90% of its original activity after incubation at 50℃ for 12 h. In addition, LipR was activated by Ca²⁺, Mg²⁺, Ba²⁺, and Sr²⁺, while strongly inhibited by Cu²⁺, Zn²⁺, Mn²⁺, and ethylenediaminetetraacetic acid. Moreover, it showed a certain tolerance to organic solvents, including acetonitrile, isopropanol, acetone, methanol, and tert-butanol. When algal oil was hydrolyzed by LipR for 24 h, there was an enrichment of n-3 long-chain polyunsaturated fatty acids, including eicosapentaenoic acid (1.22%, 1.65-fold), docosapentaenoic acid (21.24%, 2.04-fold), and docosahexaenoic acid (36.98%, 1.33-fold), and even a certain amount of diacylglycerols was also produced. As a result, LipR has great prospect in industrial applications, especially in food and/or cosmetics applications.