• Journal of Microbiology
• /
• v.35 no.4
• /
• pp.264-270
• /
• 1997

The structure of plasmid mlp1, a linear 10.2kb mitochondrial plasmid of Pleurotus ostreatus NFF A2 was determined by restriction enzyme mapping and partial sequencing. The plasmid encodes at least two proteins; a putative RNA polymerase showing homology to yeast mitochondrial RNA polymerase and to viral-encoded RNA polymerases, and a putative DNA polymerase showing significant homology to the family B thpe DNA polymerases. It also contains terminal inverted repeat sequences at both ends which are longer than 274 bp. A 1.6 kb EcoRI restriction fragment of m1p1 containing the putative RNA polymerase gene did not hybridize to the nuclear or motochondrial genomes from P. ostreatus, suggesting that it may encode plasmidspecific RNA polymerase. The gene fragment also did not hybridize with the RNA polymerase gene (RPO41) from Saccaromyces cerevisiae. The relationship between genes in m1p1 and those in another linear plasmid pC1K1 of Claviceps purpurea was examined by DNA hybridization. The result indicates that the genes for DNA and RNA polymerases are not closely related with those in C. purpurea.

• Molecules and Cells
• /
• v.37 no.5
• /
• pp.372-382
• /
• 2014

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.5
• /
• pp.828-836
• /
• 2008

The biocontrol rhizobacterium Pseudomonas sp. M18 can produce two kinds of antibiotics, namely pyoluteorin (Plt) and phenazine-1-carboxylic acid (PCA), and is antagonistic against a number of soilborne phytopathogens. In this study, a luxR-type quorum-sensing regulatory gene, vqsR, was identified and characterized immediately downstream of the Plt gene cluster in strain MI8. A vqsR-inactivated mutant led to a significant decrease in the production of Plt and its biosynthetic gene expression. However, this was restored when introducing the vqsR gene by cloning into the plasmid pME6032 in trans. The vqsR mutation did not exert any obvious influence on the production of PCA and its biosynthetic gene expression and the production of N-acylhomoserine lactones (C4 and C8-HSLs) and their biosynthetic gene rhlI expression. Accordingly, these results introduce VqsR as a regulator of Plt production in Pseudomonas spp., and suggest that the regulatory mechanism of vqsR in strain M18 is distinct from that in P. aeruginosa. In addition, it was demonstrated that vqsR mutation did not have any obvious impact on the expression of Plt-specific ABC transporters and other secondary metabolic global regulators, including GacA, RpoS, and RsmA.

• ALGAE
• /
• v.38 no.2
• /
• pp.93-110
• /
• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.

• Journal of Food Hygiene and Safety
• /
• v.27 no.4
• /
• pp.466-472
• /
• 2012

In this study, ribulose bisphosphate carboxylase (rbcL), RNApolymeraseC (rpoC1), intergenic spacer (psbA-trnH), and second internal transcribed spacer (ITS2) as identification markers for discrimination of P. mirifica in foods were selected. To be primer design, we obtained 719 bp, 520 bp, 348 bp, and 507 bp amplicon using universal primers from selected regions of P. mirifica. The regions of rbcL, rpoC1, and psbA-trnH were not proper for design primers because of high homology about P. mirifica, P. lobata, and B. superba. But, we had designed 4 pairs of oligonucleotide primers from ITS2 gene. Predicted amplicon from P. mirifica were obtained 137 bp and 216 bp using finally designed primers SFI12-miri-6F/SFI12-miri-7R and SFI12-miri-6F/SFI12-miri-8R, respectively. The species-specific primers distinguished P. mirifica from related species were able to apply food materials and processed foods. The developed PCR method would be applicable to food safety management for illegally distributed products in markets and internet shopping malls.

• Korean Journal of Plant Taxonomy
• /
• v.51 no.1
• /
• pp.109-114
• /
• 2021

Veronica nakaiana Ohwi (Plantaginaceae) is an endemic taxon on Ulleungdo Island, Korea. We report the second complete chloroplast genome sequence of V. nakaiana. Its genome size is 152,319 bp in length, comprising a large single-copy of 83,195 bp, a small single-copy of 17,702 bp, and a pair of inverted repeat regions of 25,711 bp. The complete genome contains 115 genes, including 51 protein-coding genes, four rRNA genes, and 31 tRNA genes. When comparing the two chloroplast genomes of V. nakaiana, 11 variable sites are recognized: seven SNPs and four indels. Two substitutions in the coding regions are recognized: rpoC2 (synonymous substitution) and rpl22 (nonsynonymous substitution). In nine noncoding regions, one is in the tRNA gene (trnK-UUU), one is in the intron of atpF, and seven are in the intergenic spacers (trnH-GUG~psbA, trnK-UUU, rps16~trnQ-UUG, trnC-GCA~petN, psbZ~trnG-GCC, ycf3~trnS-GGA, ycf4~cemA, and psbB~psbT). The data provide the level of genetic variation in V. nakaiana. This result will be a useful resource to formulate conservation strategies for V. nakaiana, which is a rare endemic species in Korea.

• Journal of Food Hygiene and Safety
• /
• v.27 no.3
• /
• pp.317-324
• /
• 2012

In order to determine an authenticity of food ingredient, we used DNA barcode method by universal primers. For identification of animal food ingredients, LCO1490/HCO2198 and VF2/FISH R2 designed for amplifying cytochrome c oxidase subunit1 (CO1) region and L14724/H15915 for cytochrome b (cyt b) region on mitochondrial DNA were used. Livestock (cow, pig, goat, sheep, a horse and deer) was amplified by LCO1490/HCO 2198, VF2/FISH R2 and L14724/H15915 primers. Poultry (chicken, duck, turkey and ostrich) was amplified by LCO1490/HCO 2198 and VF2/FISH R2 primers. But, Fishes (walleye pollack, herring, codfish, blue codfish, trout, tuna and rockfish) were only amplified by VF2/FISH R2 primers. For plant food ingredients, 3 types of primers (trnH/psbA, rpoB 1F/4R and rbcL 1F/724R) have been used an intergenic spacer, a RNA polymerase beta subunit and a ribulose bisphosphate carboxylase region on plastid, respectively. Garlic, onion, radish, green tea and spinach were amplified by trnH/psbA, rpoB 1F/4R and rbcL 1F/724R. The PCR product sizes were same by rpoB 1F/4R and rbcL 1F/724R but, the PCR product size using trnH/psbA primer was different with others for plants each. We established PCR condition and universal primer selection for 17 item's raw materials for foods and determine base sequences aim to PCR products in this study. This study can apply to determine an authenticity of foods through making an comparison between databases and base sequences in gene bank. Therefore, DNA barcode method using universal primers can be a useful for species identification techniques not only raw materials but also processed foods that are difficult to analyze by chemical analysis.

• Journal of Microbiology and Biotechnology
• /
• v.23 no.2
• /
• pp.189-194
• /
• 2013

In a study of hydrogen-producing bacteria, strain T4384 was isolated from rice field samples in the Republic of Korea. The isolate was identified as Enterobacter sp. T4384 by phylogenetic analysis of 16S rRNA and rpoB gene sequences. Enterobacter sp. T4384 grew at a temperature range of $10-45^{\circ}C$ and at an initial pH range of 4.5-9.5. Strain T4384 produced hydrogen at 0-6% NaCl by using glucose, fructose, and mannose. In serum bottle cultures using a complete medium, Enterobacter sp. T4384 produced 1,098 ml/l $H_2$, 4.0 g/l ethanol, and 1.0 g/l acetic acid. In a pH-regulated jar fermenter culture with the biogas removed, 2,202 ml/l $H_2$, 6.2 g/l ethanol, and 1.0 g/l acetic acid were produced, and the lag-phase time was 4.8 h. Strain T4384 metabolized the hydrolysate of organic waste for the production of hydrogen and volatile fatty acid. The strain T4384 produced 947 ml/l $H_2$, 3.2 g/l ethanol, and 0.2 g/l acetic acid from 6% (w/v) food waste hydrolysate; 738 ml/l $H_2$, 4.2 g/l ethanol, and 0.8 g/l acetic acid from Miscanthus sinensis hydrolysate; and 805 ml/l $H_2$, 5.0 g/l ethanol, and 0.7 g/l acetic acid from Sorghum bicolor hydrolysate.

• Journal of fish pathology
• /
• v.36 no.2
• /
• pp.277-286
• /
• 2023

Korean rockfish, Sebastes schlegelii, is a representative bony fish that belongs to the family Scorpaenidae and the order Scorpaeniformes. It has high ecological and economic value and is widely cultivated in many East Asian countries, including South Korea, Japan and China. One of streptococci, Streptococcus iniae, is Gram-positive cocci with a negative reaction for catalase and oxidase. The Korean rockfish shows clinical signs when infected with S. iniae, such as body darkening, bleeding, enlarged kidneys, blurred eyes, abdominal distension, etc., ultimately leading to death. The Korean rockfish causes significant economic losses every year in South Korea due to streptococcosis. In this study, we identified bacteria from the fish using polymerase chain reaction and conducted analyses of hemolytic activity and biochemical tests using API 20 STREP and API ZYM systems. Results of confirming the hemolytic activity (n=4) observed in alpha-type hemolysis (25%), beta-type hemol- ysis (50%), and gamma-type hemolysis (25%) of isolates. The biochemical test results exhibited sig- nificant variation among S. iniae. Additionally, we performed intraperitoneal injection with S. iniae in the fish and analyzed the phylogenetic tree using housekeeping genes of S. iniae, including cpsD, arcC, glnA, groEL, gyrB, mutS, pheT, prkC, rpoB, and tkt, via multilocus sequence typing (MLST). The lethal dose (LD₅₀) showed strong pathogenicity, such as 3.34 × 10 colony-forming unit (CFU)/ml for 23FBStr0601 strain and 7.16 × 10 CFU/ml for 23FBStr0602 strain. 23FBStr0603 strain showed relatively low pathogenicity at 1.73 × 10⁵ CFU/ml. The strains 23FBStr0601 and 23FBStr0602, which showed strong pathogenicity, clustered into one monophyletic group. The 23FBStr0603 strain showed weak pathogenicity and formed a monophyletic group with KCTC 3657.