• Genes and Genomics
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• v.40 no.11
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• pp.1137-1148
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• 2018

Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A+T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.

• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.445-447
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• 2018

Leuconostoc lactis CCK940, which was isolated from kimchi obtained from a Korean traditional market, produced an oligosaccharide with a degree of polymerization of more than 4. In this study, the draft genome sequence of L. lactis CCK940 was reported by using PacBio 20 kb platform. The genome of this strain was sequenced and the genome assembly revealed 2 contigs. The genome was 1,741,511 base pairs in size with a G + C content of 43.33%, containing 1,698 coding sequences, 12 rRNA genes, and 68 tRNA genes. L. lactis CCK940 contained genes encoding glycosyltransferase, sucrose phosphorylase, maltose phosphorylase, and ${\beta}$-galactosidase which could synthesize oligosaccharide.

• Journal of fish pathology
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• v.35 no.1
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• pp.129-133
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• 2022

The full genome sequence of a Korean white spot syndrome virus (WSSV, isolate: WSSV-GoC18) is presented here. We obtained a total of 12,320,554 reads with 291,172 bases, 170 gene, and 170 coding DNA sequence, which were assembled in 1 contig. Phylogenetic analysis revealed that the WSSV-GoC18 was closely related to Chinese isolate (WSSV-PC) and distinctly different with previously reported a Korean isolate (WSSV K-LV1). The complete genome sequence of WSSV isolates will be of great help in molecular epidemiological studies, contributing to molecular diagnosis and disease prevention in shrimp aquaculture.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.113.1-113
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• 2003

A potexvirus, Hosta virus X (HVX-Kr), causing mosaic and mottle symptoms was isolated from hosta plants (Hosta spp.), and its entire genome RNA sequence was determined. in Korea using cDNA library and RACE methods. The genome of HVX encodes five open reading frames coding for viral replicase, triple gene block (TGB), and viral coat protein (CP) from the 5'to 3' ends, which is a typical genome structure of potexviruses. The 3-terminal region of the virus includes the TGBI (26 kDa), TGB2 (13 kDa), TGB3 (8 kDa), and 23 kDa coat protein (CP) and the 3-nontranslated region (NTR). The CP gene of the type isolate of HVX (HVX-U) was amplified by RT-PCR and its nucleotide sequence was determined. The CPs of HVX-Kr and HVX-U had 100％ and 98.9％ identical amino acids and nucleotides, respectively. Most of the regions of the genome HVX had over 50％ nucleotide identical to other sequenced potexviruses. This is the first report of complete genome sequence information of HVX and molecular evidence supporting the virus as a distinct species of the genus Potexvirus.

• Journal of Marine Life Science
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• v.3 no.1
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• pp.1-8
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• 2018

Myosin is considered as the vital motor protein in vertebrates and invertebrates. Our present study was conducted to decipher the occurrence of myosin in dog fish (Squalus mitsukurii). We isolated one clone containing 979 bp cDNA sequence, which consisted of a complete coding sequence of 453 bp and a deduced amino acid sequence of 150 amino acids from the open reading frame with molecular weight, isoelectric point and aliphatic index are 16.72 Kda, 4.49 and 78.00, respectively. It contained 428 bp long 3' UTR with single potential polyadenylation signals (AATAAA). The predicted EF CA²⁺ binding domains were identified in residue 6-41, 83-118 and 133-150. A BLAST search indicates this protein exhibits a strong similarity to whale shark (Rhincodon typus) MLC3 (91% identical) and also house mouse (Mus musculus) MLC isoform 3f (81% identical). Phylogenetic analysis revealed that this protein is a MLC 3 isoform like protein. This protein also demonstrates highly conserved region with other myosin proteins. Homology modeling of S. mitsukuri was performed using crystal structure of Gallus gallus skeletal muscle myosin II based on high similarity. Reverse transcription-polymerase chain reaction (PCR), quantitative PCR results exhibits dogfish myosin protein is highly expressed in muscle tissue.

• Journal of Life Science
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• v.8 no.3
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• pp.263-271
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• 1998

One of the better-characterized transcription factor of E. coli is the cAMP receptor protein(CRP) and the CRP binds cAMP and DNA. The cAMP-CRP complex is involved in regulation of many genes at bacteria. The cAMP-CRP regulatory element represents, in some respects, a global regulatory network. The aim of this work was to study the structure and the mechanisms controlling the expression of CRP in Serratia marcescens. We have been get 5 different clones from Serratia which stimulated the cells to use maltose as a sole carbon source in E. coli TP2139. The crp gene clone, pCKB12, was confirmed by Southern hybridization with E. coli crp gene. The location of the crp gene was determined by construction subclones carrying various portions of pCKB12. To investigate the potential role of CRP in E. coli, lacZ fused plasmids were constructed and investigated the ${\beta}$-galactosidase activity of the fused plasmid. The Serratiamarcescens cAMP receptor protein can substitute the E. coli CRP in transcriptional activation at the lacZ gene. These results suggest that Serratia marcescens cAMP receptor protein complex functions to regulate several promoters in E. coli.

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.526-532
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• 2020

A bacterial strain, designated B301^T and isolated from raw chicken meat obtained from a local market in Korea, was characterized and identified using a polyphasic taxonomic approach. Cells were gram-negative, non-motile, obligate-aerobic coccobacilli that were catalase-positive and oxidase-negative. The optimum growth conditions were 30℃, pH 7.0, and 0% NaCl in tryptic soy broth. Colonies were round, convex, smooth, and cream-colored on tryptic soy agar. Strain B301^T has a genome size of 3,102,684 bp, with 2,840 protein-coding genes and 102 RNA genes. The 16S rRNA gene analysis revealed that strain B301^T belongs to the genus Acinetobacter and shares highest sequence similarity (97.12%) with A. celticus ANC 4603^T and A. sichuanensis WCHAc060041^T. The average nucleotide identity and digital DNA-DNA hybridization values for closely related species were below the cutoff values for species delineation (95-96% and 70%, respectively). The DNA G+C content of strain B301^T was 37.0%. The major respiratory quinone was Q-9, and the cellular fatty acids were primarily summed feature 3 (C_16:1 ω6c/C_16:1 ω7c), C_16:0, and C_18:1 ω9c. The major polar lipids were phosphatidylethanolamine, diphosphatidyl-glycerol, phosphatidylglycerol, and phosphatidyl-serine. The antimicrobial resistance profile of strain B301^T revealed the absence of antibiotic-resistance genes. Susceptibility to a wide range of antimicrobials, including imipenem, minocycline, ampicillin, and tetracycline, was also observed. The results of the phenotypic, chemotaxonomic, and phylogenetic analyses indicate that strain B301^T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter pullorum sp. nov. is proposed. The type strain is B301^T (=KACC 21653^T = JCM 33942^T).

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.1
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• pp.46-54
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• 1997

Sporulation in the fission yeast Schizosaccharomyces pombe has been regarded as an important model of cellular development and differentiation. S. pombe cells proliferate by mitosis and binary fission on growth medium. Deprivation of nutrients especially nitrogen sources, causes the cessation of mitosis and initiates sexual reproduction by malting between two sexually compatible cell types. Meiosis is then followed in a diploid cell in the absence of nitrogen source. DNA fragment complemented with the mutations of sporulation gene was isolated from the S. pombe gene library constructed in the vector, pDB 248' and designated as pDB (spo 5)1. We futher analyzed six recombinant plasmids, pDB (spo 5)2, pDB(spo 5)3, pDB(spo 5)4, pDB(spo 5)5, pDB(spo 5)6, pDB(spo 5)7, and found each plasmids is able to rescue the spo 5-2, spo 5-3, spo 5-4, spo 5-5, spo 5-6, spo 5-7, mutations, respectively. Mapping of the integrated plasmid into the homologous site of the S. pombe chromosomes demonstrated that pDB (spo 5)1, and pDB (spo 5)R1 contained the spo 5 gene. Transcipts of spo 5 gene were analyzed by Northern hybridization. Two transcripts of 3.2 kb and 25 kb were detected with 5 kb Hind III fragment containing a part of the spo 5 gene as a probe. The small mRNA (2.5 kb) appeared only when a wild-type strain was cultured in the absence of nitrogen source in which condition the large mRNA (3.2 kb) was produced constitutively. Appearance of a 2.5 kb spo 5-mRNA depends upon the function of the mei1, mei2 and mei3 genes.

• Journal of Microbiology and Biotechnology
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• v.21 no.10
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• pp.1012-1020
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• 2011

A gene coding for an endoglucanase (EglA), of the glycosyl hydrolase family 12 and derived from Aspergillus niger VTCC-F021, was cloned and sequenced. The cDNA sequence, 717 bp, and its putative endoglucanase, a 238 aa protein with a predicted molecular mass of 26 kDa and a pI of 4.35, exhibited 98.3-98.7% and 98.3-98.6% identities, respectively, with cDNA sequences and their corresponding endoglucanases from Aspergillus niger strains from the GenBank. The cDNA was overexpressed in Pichia pastoris GS115 under the control of an AOX1 promoter with a level of 1.59 U/ml culture supernatant, after 72 h of growth in a YP medium induced with 1% (v/v) of methanol. The molecular mass of the purified EglA, determined by SDS-PAGE, was 33 kDa, with a specific activity of 100.16 and 19.91 U/mg toward 1% (w/v) of ${\beta}$-glucan and CMC, respectively. Optimal enzymatic activity was noted at a temperature of $55^{\circ}C$ and a pH of 5. The recombinant EglA (rEglA) was stable over a temperature range of $30-37^{\circ}C$ and at pH range of 3.5-4.5. Metal ions, detergents, and solvents tested indicated a slightly inhibitory effect on rEglA activity. Kinetic constants ($K_m$, $V_{max}$, $k_{cat}$, and $k_{cat}/K_m$) determined for rEglA with ${\beta}$-glucan as a substrate were 4.04 mg/ml, 102.04 U/mg, 2,040.82 $min^{-1}$, and 505.05, whereas they were 10.17 mg/ml, 28.99 U/mg, 571.71 $min^{-1}$, and 57.01 with CMC as a substrate, respectively. The results thus indicate that the rEglA obtained in this study is highly specific toward ${\beta}$-glucan. The biochemical properties of rEglA make it highly valuable for downstream biotechnological applications, including potential use as a feed enzyme.