• 미생물학회지
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• 제32권4호
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• pp.264-270
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• 1994

세균의 RNA 중합효소에서 여러 ${\sigma}$ 인자들 간에 보존된 아미노산 서열중 2.3 부위와 4.2 부위의 아미노산 서열로부터 유 n하여 두가지의 PCR primer를 제작하였다. 이들을 이용하여 PCR을 수행하였을 때, E. coli와 Streptomyces coelicolor의 DNA로부터 예상되었던 480 bp 정도의 DNA가 증폭되는 것을 관찰하였다. E. coli DNA에서 증폭된 DNA를 클로닝하여 염기서열을 결정한 결과 E. coli의 rpoS 유전자로부터 유래하였음을 알았다. 이를 탐침으로 S. coelicolor에서 genomic DNA hybridization을 수행하였을 때, PvuII 절편 두가지 (3.5 kb, 2.0 kb) 와 SalI 절편 두가지(3.4kb, 1.5 kb)에 탐침이 결합하는 것을 관찰하였다. 3.5 kb의 pvuII 절편을 sublibrary로부터 클로닝하고, 탐침이 결합하는 1.0kb의 BamHI/HincII 절편의 염기서열을 분석하였다. 부분적으로 결정된 염기서열을 BLAST 프로그램을 이용하여 GenBank와 EMBL, PDB 등의 data library의 유전자들과 비교하여 본 결과Streptomyces속의 ${\sigma}$인자들을 비롯한 Synechococcus종, Anabaena종, Pseudomonas aeruginosa, Stigmatella aurantica 등의 주된 ${\sigma}$ 인자와 높은 유사성을 보였다. 현재까지 1.2 부위와 4 부위에 해당하는 부분의 염기서열을 결정하였는데, 이 부분은 S. coelicolor에서 알려진 다섯가지의 ${\sigma}$ 인자 유전자 중 hrdA와 가장 높은 유사성을 보이며, 아미노산의 유사성이 1.2부위에서는 88%, 4 부위에서는 75%인 것으로 나타났다.

• Journal of Plant Biotechnology
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• 제3권1호
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• pp.39-44
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• 2001

Plastid transformation was attempted with soybean [Glycine max (L.) Merr.] leaves and photoautotrophic and embryogenic cultures by particle bombardment using the transforming vector pZVII that carries the coding sequences for both subunits of Chlamydomonas reinhardtii Rubisco and a spectinomycin resistance gene (aadA). Spectinomycin resistant calli were selected from the bombarded leaves but the transgene was not present, indicating that the resistance was due to mutations. The Chlamydomonas rbcL and rbcS genes were shown to be site-specifically integrated into the plastid genome of the embryogenic cells with a very low transformation efficiency. None of the transformed embryogenic lines survived the plant regeneration process so no whole plants were recovered. This result does indicate that it should be possible to insert genes into the plastid genome of the important crop soybean if the overall methods are improved.

• Journal of Dairy Science and Biotechnology
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• 제38권3호
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• pp.142-145
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• 2020

Enterococcus faecalis CAUM157, isolated from raw cow's milk, is a Gram-positive, facultatively anaerobic, and non-spore-forming bacterium capable of inhabiting a wide range of environmental niches. E. faecalis CAUM157 was observed to produce a two-peptide bacteriocin that had a wide range of activity against several pathogens, including Listeria monocytogenes, Staphylococcus aureus, and periodontitis-causing bacteria. The whole genome of E. faecalis CAUM157 was sequenced using the PacBio RS II platform, revealing a genome size of 2,972,812 bp with a G+C ratio of 37.44%, assembled into two contigs. Annotation analysis revealed 2,830 coding sequences, 12 rRNAs, and 61 tRNAs. Further, in silico analysis of the genome identified a single bacteriocin gene cluster.

• Genomics & Informatics
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• 제15권4호
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• pp.170-177
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• 2017

HOTAIR is an lncRNA that has been known to have an oncogenic role in different cancers. There is limited knowledge of genetic and epigenetic elements and their interactions for the gene encoding HOTAIR. Therefore, understanding the molecular mechanism and its regulation remains to be challenging. We used different in silico analyses to find genetic and epigenetic elements of HOTAIR gene to gain insight into its regulation. We reported different regulatory elements including canonical promoters, transcription start sites, CpGIs as well as epigenetic marks that are potentially involved in the regulation of HOTAIR gene expression. We identified repeat sequences and single nucleotide polymorphisms that are located within or next to the CpGIs of HOTAIR. Our analyses may help to find potential interactions between genetic and epigenetic elements of HOTAIR gene in the human tissues and show opportunities and limitations for researches on HOTAIR gene in future studies.

• BMB Reports
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• 제31권3호
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• pp.209-220
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• 1998

How did nature create the first set of genes at the beginning of life on Earth? One of the goals of molecular biology is to elucidate the fundamental rules governing how genes and, therefore, proteins were created. Through experiments carried out in the emerging field of "in vitro" or "benchtop" evolution studies, we are gaining new insights into the origins of genes and proteins as well as the origins of their functions (e.g., catalysis). In this review, I present an overview of recent experimental approaches to the question of the origin and evolution of genes. In addition, I will introduce a novel in vitro protein emergence system that was recently developed in my laboratory.

• BMB Reports
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• 제29권3호
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• pp.183-191
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• 1996

DNA fragments, homologous to the dTDP-D-glucose 4,6-dehydratase gene, obtained from the genomic DNA of Streptomyces antibioticus $T\ddot{u}99$, a producer of the unusual macrolide antibiotic chlorothricin, were cloned and sequenced. This dehydratase gene was designated as oxil. The coding region of the oxil gene is composed of 987 bp, and analysis of the DNA sequence data reveals sequences for the gene products of 329 amino acids (molecular weight of 36,037). The deduced amino acids are 59% identical to the StrE, dTDP-D-glucose 4,6-dehydratase from the streptomycin pathway. The oxil's function was examined by expressing it in E. coli using the T7 RNA polymerase/promoter system (pRSET) to produce an active fusion protein including a his tag. This enzyme shows specificity of substrate, specific only to dTDP-D-glucose.

• BMB Reports
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• 제44권10호
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• pp.692-697
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• 2011

To investigate the pathways of oxidoreductases in plants, 2 key components in thioredox systems i.e. thioredoxin h (Trx h) and NADPH-dependent thioredoxin reductase (NTR) genes were first isolated from tomatoes (Solanum lycopersicum). Subsequently, the coding sequences of Trx h and NTR were inserted into pET expression vectors, and overexpressed in Escherichia coli. In the UV-Visible spectra of the purified proteins, tomato Trx h was shown to have a characteristic 'shoulder' at ~290 nm, while the NTR protein had the 3 typical peaks unique to flavoenzymes. The activities of both proteins were demonstrated by following insulin reduction, as well as DTNB reduction. Moreover, both NADPH and NADH could serve as substrates in the NTR reduction system, but the catalytic efficiency of NTR with NADPH was 2500-fold higher than with NADH. Additionally, our results reveal that the tomato Trx system might be involved in oxidative stress, but not in cold damage.

• ALGAE
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• 제19권4호
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• pp.283-292
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• 2004

Psilothallia is a ceramiaceous red algal. genus that includes three species worldwide: P. dentate, P. siliculosa, and P. striate. The latter two species are limited to Australian waters, and P. dentate occurs in Japan. We here report the detailed morphology of P. dentate, and also determined plastid protein-coding psbA in P. dentate and putative relatives. Psilothallia dentate is distinguished by compressed thalli with alternate-distichous determinate branchlets, six periaxial cells, rhizoidal filaments in axes, cystocarps with 7-8 involucral filaments, spermatangia on branched filaments, and tetrahedrally divided tetrasporangia on branched filaments. Psilothallia dentate is also unusual in that cystocarps, spermatangial clusters, and tetrasporangial tufts are formed on short adventitious indeterminate branches arising on axils of determinate branchlets. The phylogenetic trees of psbA sequences show that P. dentata was nested in a monophyletic Glade comprising Ptilota, Neoptilota, and Plumaria. This result suggests that the taxonomic position of P. dentate may be transferred from the tribe Rhodocallideae to the Ptiloteae.

• Journal of Microbiology and Biotechnology
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• 제28권9호
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• pp.1542-1546
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• 2018

Bacterial canker in kiwifruit is caused by Pseudomonas syringae pv. actinidiae (Psa). In this study, the bacteriophage PPPL-1 effective against Psa was characterized. Belonging to the Podoviridae family, PPPL-1 was effective against most Psa strains as well as most Pseudomonas syringae pathovars. PPPL-1 carries a 41,149-bp genome with 49 protein coding sequences and is homologous to the previously reported phiPSA2 bacteriophage. The lytic activity of PPPL-1 was stable up to $40^{\circ}C$, within a range of pH 3-11 and under 365 nm UV light. These results indicate that the bacteriophage PPPL-1 might be useful to control Psa in the kiwifruit field.

• 산업기술연구
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• 제28권B호
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• pp.53-57
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• 2008

From the extensive screening for small cryptic plasmid among about 23 lactic acid bacteria (LAB), 2.4 kb of cryptic plasmid was isolated from Lactobacillus farciminis strain KCTC 3681 and named as pLF24. The plasmid pLF24 was a circular molecule of 2,396 base-pairs in length with a G+C content of 38%. Two protein-coding sequences could be predicted. ORF1 and ORF2 showed homologies to plasmids of gram-positive bacteria. The replication protein coded by ORF2 and the plus origin, were similar to replication regions of other gram-positive bacteria as shown in plasmids such as pLH2, pLS141-1 and pLC2. The nucleotide sequence of pLF24 was deposited into Genbank data base with an accession number of EU429343. The newly isolated plasmid can be used for construction of shuttle vector in Lactobacillus bacteria.