• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.911-917
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• 2022

As valuable antibiotics, microbial natural products have been in use for decades in various fields. Among them are polyene compounds including nystatin, amphotericin, and nystatin-like Pseudonocardia polyenes (NPPs). Polyene macrolides are known to possess various biological effects, such as antifungal and antiviral activities. NPP A1, which is produced by Pseudonocardia autotrophica, contains a unique disaccharide moiety in the tetraene macrolide backbone. NPP B1, with a heptane structure and improved antifungal activity, was then developed via genetic manipulation of the NPP A1 biosynthetic gene cluster (BGC). Here, we generated a Streptomyces artificial chromosomal DNA library to isolate a large-sized NPP B1 BGC. The NPP B1 BGC was successfully isolated from P. autotrophica chromosome through the construction and screening of a bacterial artificial chromosome (BAC) library, even though the isolated 140-kb BAC clone (named pNPPB1s) lacked approximately 8 kb of the right-end portion of the NPP B1 BGC. The additional introduction of the pNPPB1s as well as co-expression of the 32-kb portion including the missing 8 kb led to a 7.3-fold increase in the production level of NPP B1 in P. autotrophica. The qRT-PCR confirmed that the transcription level of NPP B1 BGC was significantly increased in the P. autotrophica strain containing two copies of the NPP B1 BGCs. Interestingly, the NPP B1 exhibited a previously unidentified SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibition activity in vitro. These results suggest that the Streptomyces BAC cloning of a large-sized, natural product BGC is a valuable approach for titer improvement and biological activity screening of natural products in actinomycetes.

• Genomics & Informatics
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• v.16 no.2
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• pp.22-29
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• 2018

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

• Journal of Microbiology
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• v.39 no.1
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• pp.37-41
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• 2001

The fission yeast Schizosaccharomyces pombe contains two distinct superoxide dismutase (SOD) activities, one in the cytosol encoded by the $sod2^{+}$ gene and the other in mitochondria. The $sod2^{+}$ gene encoding putative mitochondrial manganese superoxide dismutase (MnSOD) was isolated from the S. pombe genomic library using a PCR fragment as the probe. The nucleotide sequence of the $sod2^{+}$ gene and its flanking region (4051 bp HindIII fragment) was determined. An intron of 123 nt in size was predicted and confirmed by sequencing the cDNA following reverse transcription PCR. The predicted Sod2p consists of 218 amino acid residues with a molecular mass of 24,346 Da. The deduced amino acid sequence showed a high degree of homology with other MnSODs, especially in the metal binding residues at the active site and their relative positions. The transcriptional start site was mapped by primer extension at 231 at upstream from the ATG codon. A putative TATA box(TATAAAA) was located 58 nt upstream from the transcriptional start site and putative polyadenylation sites were located at 1000, 1062, and 1074 nt downstream from the ATG start codon.

• Microbiology and Biotechnology Letters
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• v.44 no.2
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• pp.140-144
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• 2016

The gene encoding chondroitinase ABC from a genomic library of Bacteroides stercoris HJ-15, which was isolated from human feces, was cloned. The cloned gene consisted of 3,090 bp and was predicted to encode a 1,029−amino-acid protein. The B. stercoris chondroitinase ABC gene was not homologous to other chondroitinase ABC genes; however, its amino acid sequence showed 71% homology to that of Bacteroides thetaiotaomicron. The gene was cloned in the pET-26b+ expression vector and expressed under the T7 promoter in Escherichia coli BL21(DE3). The purified recombinant chondroitinase ABC degraded chondroitin sulfates A, B, and C.

• Proceedings of the Korean Society of Toxicology Conference
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• 2000.11a
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• pp.31-41
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• 2000

The major issue in the post genome sequencing era is determination of gene expression patterns in variety of biological systems. A microarray system is a powerful technology for analyzing the expression profile of thousands of genes at one experiment. In this study, we constructed cDNA microarray which carries 2,304 cDNAS derived from oligo-capped mouse cDNA library. Using this hand-made microarray we determined gene expression in various biological systems. To determine tissue specific genes, we compared Nine genes were highly-expressed in adult mouse brain compared to kidney, liver, and skeletal muscle. Tissue distribution analysis using DNA microarray extracted 9 genes that were predominantly expressed in the brain. A database search showed that five of the 9 genes, MBP, SC1, HiAT3, S100 protein-beta, and SNAP25, were previously known to be expressed at high level in the brain and in the nervous system. One gene was highly sequence similar to rat S-Rex-s/human NSP-C, suggesting that the gene is a mouse homologue. The remaining three genes did not match to known genes in the GenBank/EMBL database, indicating that these are novel genes highly-expressed in the brain. Our DNA microarray was also used to detect differentiation specific genes, hormone dependent genes, and transcription-factor-induced genes. We conclude that DNA microarray is an excellent tool for identifying differentially expressed genes.

• Journal of Plant Biotechnology
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• v.35 no.2
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• pp.95-100
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• 2008

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a main enzyme in the glycolytic pathway, is involved in cellular energy production and regarded as a housekeeping gene. Previously, cytosolic GAPDH was selected as the most significantly abundant gene in EST library of sweetpotato suspension cells. In this study, a full-length of cDNA clone (IbGAPDH) encoding GAPDH was isolated from suspension-cultured cells of sweetpotato (Ipomoea babatas), and its expression was investigated with a view to understanding the physiological function of GAPDH in relation to environmental stresses. IbGAPDH encoded a 36.9 kDa polypeptide consisting of 337 amino acids. When the deduced amino acid of IbGAPDH was compared with other higher plants, IbGAPDH showed high homology with cytosolic GAPDH. The mRNA level of IbGAPDH significantly increased under environmental stresses, such as $H_2O_2$, MV and cold treatments. Among them, the transcript level of IbGAPDH gene was the highest under cold stress. Further investigation of the transcription level under $10^{\circ}C$ or $15^{\circ}C$ was performed with different tissues of sweetpotato. The transcription of IbGAPDH was increased by cold stress with tissue-specificity, moreover, showed different patterns according to temperature.

• Proceedings of the Korean Society of Crop Science Conference
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• 2002.05a
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• pp.48-50
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• 2002

A strategy for development of a functional rice in proved with human lactoferrin and enhancement of nutrient compounds was planned. For the purposes we have cloned and characterized a human lactoferrin cDNA from human mammary gland cDNA library A endosperm storage vacuole targeting sequence and the cDNA fragment was linked to endosperm specific glutelin promoter. The fusion gene fragment was inserted into a binary vector containing MAR gene. In addition a new ${\beta}$-galactosidase gene from Bifidobacterium of human was used as a reporter gene in the vector system, Rice plants showing a high concentration of amino acids in the endosperm cells were developed by using a biochemical mutation and bred for the transformation with the binary vector system Finally we have established a transformation method for the rice endosperm cells.

• Journal of Microbiology and Biotechnology
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• v.4 no.4
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• pp.256-263
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• 1994

The aceB gene, encoding for malate synthase, one of the key enzymes of glyoxylate bypass, was isolated from a pMT1-based Corynebacterium glutamicum gene library via complementation of an Escherichia coli aceB mutant on an acetate minimal medium. The aceB gene was closely linked to aceA, separated by 598 base pairs, and transcribed in divergent direction. The aceB expressed a protein product of Mr 83, 000 in Corynebacterium glutamicum which was unusually large compared with those of other malate synthases. A DNA-sequence analysis of the cloned DNA identified an open-reading frame of 2, 217 base pairs which encodes a protein with the molecular weight of 82, 311 comprising 739 aminoo acids. The putative protein product showed only limited amino acid-sequence homology to its counteliparts in other organisms. The N-terminal region of the protein, which shows no apparent homology with the known sequences of other malate synthases, appeared to be responsible for the protein s unusually large size. A potential calciumbinding domain of EF-hand structure found among eukaryotes was detected in the N-terminal region of the deduced protein.

• Journal of Microbiology and Biotechnology
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• v.19 no.9
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• pp.881-887
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• 2009

Forty-four eicosapentaenoic acid (EPA)-producing microbial strains were isolated from the intestines of marine fishes. Among them, one strain showing a maximum level of EPA (4.78% of total fatty acids) was identified as Shewanella sp. BR-2 on the basis of its 168 rRNA sequence. The EPA content reached a maximum level during the mid-exponential phase of cell growth, and gradually decreased with further growth of the cells. A cosmid DNA including the EPA biosynthesis gene cluster consisting of pfaA-E was isolated from a cosmid library of genomic DNA of Shewanella sp. BR-2, named pCosEPA-BR2. An E. coli clone harboring pCosEPA-BR2 produced EPA at a maximum level of 7.5% of total fatty acids, confirming the EPA biosynthesis activity of the cloned gene cluster.

• Korean Journal of Microbiology
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• v.24 no.4
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• pp.357-363
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• 1986

Synthesis of threonine and methionine in yeast, Saccharomyces cerevisiae shares a common pathway from aspartate via homoserine. HOM6 gene encodes homoserine dehydrogenase (HSDH) which catalyzes the inter-conversion of beta-aspartate semialdehyde and homoserine. The level of HSDH is under methionine specific control. A recombinant plasmid (pEK1: 13.3kb), containing HOM6 gene, has been isolated and cloned into E. coli by complenemtary transformation of a homoserine auxotrophic yeast strain M-20-20D (hom6, trp1, ura3) to a prototrophic M20-20D/pEK1, using a library of yeast genomic DNA fragments in a yeast centromeric plasmid, YCp50(8.0kb). Isolation of HOM6has been primarily confirmed by retransformation of the original yeast strain M20-20D, using the recombinant plasmid DNA which was extracted from M20-20D/pEK1 and subsequently amplified in E. coli. Eleven cleavage sites in the insery (5.3kb) have been localized through fragment analysis for 8 restriction endonucleases; Bgl II(2 site), Bgl II(1), Cla I(3), Eco RI(1), Hind III(2), Kpn I (1), Pvu II(1) and Xho I(1).