• Korean Journal of Microbiology
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• v.54 no.2
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• pp.152-154
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• 2018

Klebsiella pneumoniae is a Gram-negative, rod-shape bacterium causing disease in human and animal lungs. K. pneumoniae has been often found to gain antimicrobial resistance, thus it has been difficult to treat K. pneumoniae infection with antibiotics. For such infection, bacteriophage can provide an alternative approach for pathogenic bacterial infection with antimicrobial resistance, because of its sensitivity and specificity to the host bacteria. Bacteriophage KP1 was isolated in sewage and showed specific infectivity to K. pneumoniae. Here, we report the draft genome sequence of Klebsiella pneumoniae phage KP1. The draft genome of KP1 is 167,989 bp long, and the G + C content is 39.6%. The genome has 295 predicted ORFs and 14 tRNA genes. In addition, it encodes various enzymes which involve in lysis of the host cell such as lysozyme and holin.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.35 no.6
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• pp.676-681
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• 2002

Different types of transcripts encoding growth hormone (GH) were identified from cDNA libraries constructed with pituitaries of a marine fish species, greenling (Hexagrammos otakii). GH-homologous cDNA clones were isolated using the high-density filter hybridization and the expressed sequence tag techniques. Of 39 full-length positive cDNA clones, 31 clones ($79\%$) displayed an identical sequence, however, remaining 8 clones exhibited several polymorphisms in their sequences including (1) the length and sequence variability in the 5' upstream region, (2) insertional sequences in open reading frame, and (3) deletion and/or single nucleotide polymorphism in the untranslated 3' region. Based on RT-PCT and RNA dot blot analyses, these transcripts were proven to be expressed in a pituitary-specific manner.

• Applied Biological Chemistry
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• v.40 no.5
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• pp.380-387
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• 1997

Phytopathogenic Erwinia carotovora subsp. carotovora (Ecc) LY34 causes plant tissue maceration by secretion of pectinolytic enzymes such as pectate Iyase (PL) existed as multiple isoenzyme form. Genomic DNA from Ecc LY34 was digested with Sau3Al and ligated into the BamHI site of pBluescript ll $SK^+$. Among them, a clone hydrolyzing polypectate was selected and its DNA was digested with BamHI. Through the subsequent subcloning the resulting 3.1 kb fragment, corresponding to a peICI, was subcloned into pLYPA 100. The structural organization of a peICI gene encoding a 374 amino acid residues consists of an open reading frame (ORF) of 1,122 bp commencing with a ATG start codon and followed by a TAA stop codon. PeICI contained a typical prokaryotic signal peptide of 22-amino acid. Since the deduced amino acid sequences of PeICl protein was very similar to those of PelIII of Erwinia carotovora subsp. carotovora, and to those of Pel3 of Erwinia carotovora subsp. atroseptica, and to those of PeIC of Erwinia carotovora subsp. carotovora, it belong to the same family PLbc group. The 374-amino acld PeICI had a calculated Mr of 40,507 and pI of 7.60.

• BMB Reports
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• v.44 no.10
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• pp.653-658
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• 2011

Sclerotinia sclerotiorum fungus has three endoxylanases induced by wheat bran. In the first part, a partial xylanase sequence gene (90 bp) was isolated by PCR corresponding to catalytic domains (${\beta}5$ and ${\beta}6$ strands of this protein). The high homology of this sequence with xylanase of Botryotinia fuckeliana has permitted in the second part to amplify the XYN1 gene. Sequence analysis of DNA and cDNA revealed an ORF of 746 bp interrupted by a 65 bp intron, thus encoding a predicted protein of 226 amino acids. The mature enzyme (20.06 kDa), is coded by 188 amino acid (pI 9.26). XYN1 belongs to G/11 glycosyl hydrolases family with a conserved catalytic domain containing $E_{86}$ and $E_{178}$ residues. Bioinformatics analysis revealed that there was no Asn-X-Ser/Thr motif required for N-linked glycosylation in the deduced sequence however, five O-glycosylation sites could intervene in the different folding of xylanses isoforms and in their secretary pathway.

• Journal of Microbiology and Biotechnology
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• v.19 no.2
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• pp.121-127
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• 2009

Sequencing analysis of a 5-kb DNA fragment from Streptomyces venezuelae ATCC 15439 revealed the presence of one 3.1-kb open reading frame(ORF), designated as afsR-sv. The deduced product of afsR-sv(1,056 aa) was found to have high homology with the global regulatory protein AfsR. Homology-based analysis showed that aftR-sv represents a transcriptional activator belonging to the Streptomyces antibiotic regulatory protein(SARP) family that includes an N-terminal SARP domain containing a bacterial transcriptional activation domain(BTAD), an NB-ARC domain, and a C-terminal tetratricopeptide repeat domain. Gene expression analysis by reverse transcriptase PCR(RT-PCR) demonstrated the activation of transcription of genes belonging to pikromycin production, when aftR-sv was overexpressed in S. venezuelae. Heterologous expression of the aftR-sv in different Streptomyces strains resulted in increased production of the respective antibiotics, suggesting that afsR-sv is a positive regulator of antibiotics biosynthesis.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.579-586
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• 2010

A genomic DNA fragment encoding a putative maltooligosyltrehalose synthase (NfMTS) for trehalose biosynthesis was cloned by the degenerate primer-PCR from cyanobacterium Nostoc flagelliforme. The ORF of NfMTS was 2,799 bp in length and encoded 933 amino acid residues constituting a 106.6 kDa protein. The deduced amino acid sequence of NfMTS contained 4 regions highly conserved for MTSs. By expression of NfMTS in E. coli, it was demonstrated that the recombinant protein catalyzed the conversion of maltohexaose to maltooligosyl trehalose. The $K_m$ of the recombinant enzyme for maltohexaose was 1.87 mM and the optimal temperature and pH of the recombinant enzyme was at $50^{\circ}C$ and 7.0, respectively. The expression of MTS of N. flagelliforme was upregulated, and both trehalose and sucrose contents increased significantly in N. flagelliforme during drought stress. However, trehalose accumulated in small quantities (about 0.36 mg/g DW), whereas sucrose accumulated in high quantities (about 0.90 mg/g DW), indicating both trehalose and sucrose were involved in dehydration stress response in N. flagelliforme and sucrose might act as a chemical chaperone rather than trehalose did during dehydration stress.

• Journal of agriculture & life science
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• v.46 no.2
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• pp.129-137
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• 2012

A carboxymethyl cellulase gene, cel5B, was cloned, sequenced, and expressed in Escherichia coli. pRCS20 in E. coli was identified from metagenomic cosmid library of cow rumen for cellulase activity on a carboxymethyl cellulose agar plates. Cosmid clone (RCS20) was partially digested with Sau3AI, ligated into BamHI site of pBluescript II SK+ vector, and transformed into E. coli $DH5{\alpha}$. The insert DNA of 1.3 kb was obtained, designated cel5B, which has the activity of hydrolyzation of CMC. The cel5B gene had an open reading frame (ORF) of 1,059 bp encoding 352 amino acids with a signal peptide of 48 amino acids and the conserved region, VIYEIYNEPL, belongs to the glycosyl hydrolase family 5. The molecular mass of Cel5B protein expressed from E. coli $DH5{\alpha}$ exhibited to be about 34 kDa by CMC-SDS-PAGE. The optimal pH was 8.0, and the optimal temperature was about $50^{\circ}C$ for its enzymatic activity.

• Microbiology and Biotechnology Letters
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• v.48 no.4
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• pp.480-490
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• 2020

A novel lipase gene, Lip-1420, was isolated from a metagenomic library constructed from reed marsh from Mt. Jumbong in Korea, comprising 112,500 members of recombinant plasmids. The DNA sequence of Lip-1420-subclone (5,513 bp) was found to contain at least 11 ORFs according to the GenBank database. The ORF-3 gene was inserted into the pET21a plasmid containing the C-terminal 6-His tag and transformed into E. coli BL21(DE3) to express the recombinant lipase protein. Lip-1420 was purified using a fast protein liquid chromatography system. The gene was registered in GenBank (MH628529). The values of Km and Vmax were determined as 0.268 mM and 1.821 units, respectively, at 40℃ and pH 8.0, using p-nitrophenyl palmitate as the substrate. This lipase belongs to family IV taxonomically because it has conserved HGGG and GDSAG motifs in the constitutive amino acid sequence. According to the predicted structural model, the binding sites are represented by residues H78, G81, D150, S151, A152, V181, and D236. Finally, Lip-1420 showed triolein selectivity for methanolysis between triolein (18:1) and tristearin (18:0) substrates. Further study of the selective mechanism and structure-function relationship of this new lipase could be useful for more practical applications.

• Journal of fish pathology
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• v.35 no.1
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• pp.121-128
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• 2022

Recent studies revealed that histone proteins are involved in innate immune responses during pathogen invasion as well as DNA packing. This study characterized the histone genes (H2A.V) of sevenband groupers and analyzed gene expression in NNV-infected sevenband groupers. The open reading frame (ORF) of H2A.V is 387 bp which encoded 128 amino acid residues. The deduced amino acid sequence of H2A.V harbor a highly conserved domain for H2A/H2B/H3 and H2A_C binding domain. Quantitative real-time PCR analysis showed that H2A.V had a high gene expression level in the brain and blood after being NNV-infected. An increase in extracellular histone protein in the blood has been identified as a biomarker for vascular function in humans. More research is required to understand histone's immune response at the protein level or in aquatic animals.

• Journal of Life Science
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• v.22 no.4
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• pp.437-446
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• 2012

A metagenomic library of cow rumen in the pCC1FOS phage vector was screened in $E.$ $coli$ EPI300 for cellulase activity on carboxymethyl cellulose agar plates. One clone was partially digested with $Sau$3AI, ligated into the $Bam$HI site of the pBluescript II SK+ vector, and transformed into $E.$ $coli$ $DH5{\alpha}$. We obtained a 1.5 kb insert DNA, designated $cel$5C, which hydrolyzes carboxymethyl cellulose. The cel5C gene has an open reading frame (ORF) of 1,125 bp encoding 374 amino acids. It belongs to the glycosyl hydrolase family 5 with the conserved domain LIMEGFNEIN. The molecular mass of the Cel5C protein induced from $E.$ $coli$ $DH5{\alpha}$, as analyzed by CMC SDS-PAGE, appeared to be approximately 42 kDa. The enzyme showed optimum cellulase activity at pH 4.0, and $50^{\circ}C$. We examined whether the $cel$5C gene comes from the 49 identified cow rumen bacteria using PCR. No PCR bands were identified, suggesting that the $cel$5C gene came from the unidentified cow rumen bacteria.