• Journal of Microbiology
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• v.33 no.3
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• pp.252-259
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• 1995

The PCR was employed to detect and characterize the bovine immunodeficiency-like virus (BIV), which is a newly recognized member of the I entivirinae of the retroviruses. Degenerate primers representing the conserved regions in the pol genes of the Lentivirinae, were used to detect proviral DNA obtained from the bovine embryonic spleen cell cultures infected with BIV. The PCR amplified DNA fragment was molecularly cloned and sequenced. The BIV DNA fragment contained a sequence identical to that reported by Garvey et al. (Garvey et al., 1990. Virology, 175, 391-409). With the degenerate primers, peripheral blood mononuclear cells (PBMCs) of sick cattle and cells cultured with BIV were tested to determine genetic variation of BIV pol conserved sequence. We found the sequence heterogeneity within cultures and most variations occurred at the third base of codons that would not lead to amino acid substitutions. Another change was GAG (Glu) to AAG (Lys) within the BIV isolates. Interestingly, the altered sequence is also found in other lentiviruses such as HIV-2, SIV mac, CAEV and EIAV.

• Journal of Plant Biotechnology
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• v.49 no.1
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• pp.15-29
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• 2022

Cyclophilins (CYPs) are highly conserved ubiquitous proteins belong to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily. These proteins are present in a wide range of organisms; they contain a highly conserved peptidyl-prolyl cis/trans isomerase domain. A comprehensive database survey identified a total of 35 genes localized in all cellular compartments of Solanum lycopersicum L., but largely in the cytosol. Sequence alignment and conserved motif analyses of the SlCYP proteins revealed a highly conserved CLD motif. Evolutionary analysis predicted the clustering of a large number of gene pairs with high sequence similarity. Expression analysis using the RNA-Seq data showed that the majority of the SlCYP genes were highly expressed in mature leaves and blooming flowers, compared with their expression in other organs. This study provides a basis for the functional characterization of individual CYP genes in the future to elucidate their role(s) in protein refolding and long-distance signaling in tomatoes and in plant biology, in general.

• Genomics & Informatics
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• v.6 no.2
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• pp.72-76
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• 2008

Hypoxia-inducible factor $1{\alpha}\;(HIF1{\alpha})$ is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ is responsible for the negative regulation of $HIF1{\alpha}$ in normoxia. The interactions of the $HIF1{\alpha}$ ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD(NODD and CODD). Multiple sequence alignment with $HIF1{\alpha}$ homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the $HIF1{\alpha}$ CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of $HIF1{\alpha}$ for the recognition of p53.

• Microbiology and Biotechnology Letters
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• v.30 no.2
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• pp.105-110
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• 2002

The sequence of 3,221 nucleotides immediately adjacent to rpsA gene encoding 30S ribosomal protein S1 of Brevibacterium ammoniagenes was determined. A putative open reading frame (ORF) of 2,670 nucleotides for a polypeptide of 889 amino acid residues and a TAG stop codon was found, which is located at a distance of 723 nucleotides upstream from rpsA gene with same translational direction. The deduced amino acid sequence of the ORF was found to be highly homologous to the DNA polymerase I of Streptomyces griseus (75.48％), Rhodococcus sp. ATCC 15963 (56.69％), Mycobacterium tuberculosis (55.46％) and Mycobacterium leprae (53.99％). It was suggested that the predicted product of the ORF is a DNA polymerase I with three functional domains. Two domains of 5 → 3 exonuclease and DNA polymerase are highly conserved with other DNA polymerase I, but 3 → 5 exonuclease domain is less conserved.

• Journal of Microbiology and Biotechnology
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• v.8 no.4
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• pp.310-317
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• 1998

Peptide synthetases are large multifunctional enzyme complexes that catalyze the nonribosomal synthesis of a structurally diverse family of peptide antibiotics. These enzymes are composed of functionally independent domains with independent enzymatic activities. Their specific linkage order of domains forms the protein template that defines the sequence of the incorporated amino acids. Within each domain, several motifs of highly conserved sequences have been identified from the sequence alignment of the various peptide synthetases ［30］. Taking advantage of the conserved nucleotide sequence of Core 1 and Core 2, we designed PCR primers to amplify the peptide synthetase genes from three different gram-positive bacterial strains. Nucleotide sequence analysis of the amplified PCR products from those three strains showed significant homology to various peptide synthetase genes, suggesting that the PCR products are parts of peptide synthetase genes. Therefore, this rapid and efficient PCR technique can be used for the isolation of peptide synthetase genes from various strains.

• Journal of Ginseng Research
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• v.37 no.2
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• pp.227-247
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• 2013

MicroRNAs (miRNAs) are a class of recently discovered non-coding small RNA molecules, on average approximately 21 nucleotides in length, which underlie numerous important biological roles in gene regulation in various organisms. The miRNA database (release 18) has 18,226 miRNAs, which have been deposited from different species. Although miRNAs have been identified and validated in many plant species, no studies have been reported on discovering miRNAs in Panax ginseng Meyer, which is a traditionally known medicinal plant in oriental medicine, also known as Korean ginseng. It has triterpene ginseng saponins called ginsenosides, which are responsible for its various pharmacological activities. Predicting conserved miRNAs by homology-based analysis with available expressed sequence tag (EST) sequences can be powerful, if the species lacks whole genome sequence information. In this study by using the EST based computational approach, 69 conserved miRNAs belonging to 44 miRNA families were identified in Korean ginseng. The digital gene expression patterns of predicted conserved miRNAs were analyzed by deep sequencing using small RNA sequences of flower buds, leaves, and lateral roots. We have found that many of the identified miRNAs showed tissue specific expressions. Using the insilico method, 346 potential targets were identified for the predicted 69 conserved miRNAs by searching the ginseng EST database, and the predicted targets were mainly involved in secondary metabolic processes, responses to biotic and abiotic stress, and transcription regulator activities, as well as a variety of other metabolic processes.

• Bulletin of the Korean Chemical Society
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• v.18 no.8
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• pp.798-800
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• 1997

• Journal of Microbiology and Biotechnology
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• v.24 no.1
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• pp.70-79
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• 2014

In an attempt to develop a variety of expression vector systems for Corynebacterium glutamicum, six types of promoters, including $P_{tac}$, $P_{sod}$, $P_{sod}$ with a conserved Shine-Dalgarno (SD) sequence from C. glutamicum, $P_{ilvC}$, $P_{ilvC}$ with a conserved SD-1 ($P_{ilvC-M1}$), and $P_{ilvC}$ with a conserved SD-2 ($P_{ilvC-M2}$), were cloned into a modified shuttle vector, pCXM48. According to analysis of promoter strength by quantitative reverse transcription PCR, $P_{sod}$ and $P_{sod-M}$ were superior to tac and ilvC promoters in terms of transcription activity in C. glutamicum. All of the promoters have promoter activities in Escherichia coli, and $P_{sod-M}$ displayed the highest level of transcriptional activity. The protein expression in constructed vectors was evaluated by measuring the fluorescence of green fluorescent protein (GFP) and SDS-PAGE. C. glutamicum harboring plasmids showed GFP fluorescence with an order of activity of $P_{ilvC}$ > $P_{ilvC-M1}$ > $P_{sod}$ > $P_{ilvC-M2}$ > $P_{sod-M}$, whereas all plasmids except pCSP30 with $P_{sod}$ displayed fluorescence activities in E. coli. Of them, the strongest level of GFP was observed in E. coli with $P_{sod-M}$, and this seems to be due to the introduction of the conserved SD sequence in the translational initiation region. These results demonstrate that the expression vectors work well in both C. glutamicum and E. coli for the expression of target proteins. In addition, the vector systems harboring various promoters with different strengths, conserved SD sequences, and multiple cloning sites will provide a comfortable method for cloning and gene expression, and consequently contribute to the metabolic engineering of C. glutamicum.

• Biomolecules & Therapeutics
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• v.9 no.2
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• pp.79-87
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• 2001

Heat shock proteins serve as chaperone by preventing the aggregation of denatured proteins and promote survival of pathogens in harsh environments. In this study, heat shock gene encoding a 84-kDa (p84) protein, which is one of the three major heat shock proteins in S. pneumoniae, was cloned and characterized. PCR with a forward primer derived from N-terminal amino acid sequence of the p84 and a reverse primer derived from the conserved second ATP-binding region of Clp family was used for amplification of the gene encoding the p84 and subsequently the PCR product was used for sequence determination. Sequence analysis of the p84 gene demonstrated that it is a member of ClpL. The deduced amino acid sequence of pneumococcal ClpL shows homology with other members of the Clp family, and particularly, even in variable leader region, with bovine Clp-like protein and L. lactis ClpL. S. pneumoniae clpL is the smallest clop member (701 amono acids) containing the two conserved ATP-binding regions, and hydrophilic N-terminal variable region of pneu-mococcal Clp ATPase is much shorter than any known Clp ATPases. Histidine tagged ClpL was overexpressed and purified from E. coli. Immunoblot analysis employing antisera raised against pneumococcus p84 demonstrated no cross-reactivity with Clp analog in Eschericha coli, Staphylococcus aureus and human HeLa cells. Preimmunization of mice with ClpL extended mice life partially but did not protect them from death.

• Parasites, Hosts and Diseases
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• v.34 no.2
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• pp.127-134
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• 1996

Twelve isolates of Accnthamoebc app. assigned to either A. castellanii or A. poIMphoSa, and type strains of A. culbefsoni, A. henIWi, A. pqkestinefiE, and A. astronyxi,s were examined by restriction fragment length polymorphism (RFLP) of a conserved region of small subunit ribosomal RMh gene (ssu rDNA) amplified by polymerase chain reaction (PCR). The PCR products of the isolates measured approximately 910-930 bp, except for that of A. astronyxis which was extraordinarily long, approximately 1,170 bp. Average of estimated sequence divergence of the amplified DNA among the isolates assigned to A. castellanii was 9.8% whereas that among the isolates assigned to A. polvphusn 9.6%. The maximum intraspecific sequence divergence among the isolates assigned to A. costellanii was observed between the Chang and Ma strains (17.3%) while that among the isolates assigned to A. poIWphosa was observed between KA/S3 and KA/S7 strains (16.1%). The both maximum sequence divergences were much greater than the minimum interspecific sequence divergence between A. cnstellnnii and A. polwphasa (2.6%) which appeared between the Castellani (or CCAP 1501/12 g) and KA/S3 strains. The PCR-RFLP patterns of A. culbertsoni, A. healyi, A. palestinensis, and A. ostronvxis were quite diverse from one another and from those of isolates assigned to either A. castellanii or A. polyphoga. It is suggested that taxonomic validity of the isolates assigned to either A. castellnnii or A. polyphoga should be reevaluated.