• 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 Microbiology and Biotechnology
• /
• v.21 no.4
• /
• pp.421-429
• /
• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• 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.

• Tuberculosis and Respiratory Diseases
• /
• v.55 no.1
• /
• pp.41-58
• /
• 2003

Background : The resurgence of tuberculosis and the widespread emergence of multidrug-resistant M. tuberculosis have emphasized the importance of rapid and accurate diagnostic procedures. Recently, the oligonucleotide chip has proven to be a useful tool in the rapid diagnosis of infectious diseases. The purpose of this study was to rapidly and accurately detect specific mutations in the rpoB, katG and rpsL genes associated with rifampin, isoniazid and streptomycin resistance in M. tuberculosis, respectively, using a single oligonucleotide chip. Method : For detection of drug-resistance, 7 wild-type and 13 mutant-type probes for rifampin, 2 wild-type and 3 mutant-type probes for isoniazid, and 2 wild-type and 2 mutant-type probes for streptomycin were designed and spotted onto glass slides. Fifty-five cultured samples of M. tuberculosis were amplified by PCR, and then underwent hybridization and scanning. Direct sequencing was done to verify the results from the oligonucleotide chip and to analyze the types of mutations. Result : Thirty-five cases out of 40 rifampin-resistant strains(~88%) had mutations in the rpoB gene. One case had a new mutation(D516F, GAC R TTC) and another known mutation together. Twenty cases out of 42 isoniazid-resistant strains(~50%) had mutations in the katG gene, while 7 cases out of 9 streptomycin-resistant strains(~78%) had mutations in the rpsL gene. From these results, the oligonucleotide chip was confirmed to be able to detect the most frequent mutations from the genes associated with rifampin, isoniazid and streptomycin resistance. The results proved that the drug-resistance detection probes were specific. When the results from the oligonucleotide chip and DNA sequencing were compared, the types of mutations were exactly matched. Conclusion : The diagnostic oligonucleotide chip with mutation specific probes for drug resistance is a very reliable and useful tool for the rapid and accurate diagnosis of drug resistance against rifampin, isoniazid and streptomycin in M. tuberculosis infections.

• Tuberculosis and Respiratory Diseases
• /
• v.72 no.2
• /
• pp.173-176
• /
• 2012

We report a rare case of lung disease caused by Mycobacterium terrae in a previously healthy woman. A 45-year-old woman was referred to our hospital due to a chronic cough with sputum. A computed tomography scan of the chest revealed bronchiolitis in conjuction with bronchiectasis in both lungs. Nontuberculous mycobacteria were identified and isolated from the bronchoalveolar lavage fluid collected from each lung. All isolates were identified as M. terrae by various molecular methods that characterized the rpoB and hsp65 gene sequences. Antibiotic therapy using clarithromycin, rifampin, and ethambutol improved the patient's condition and successfully resulted in sputum conversion.

• Journal of Microbiology
• /
• v.40 no.3
• /
• pp.237-240
• /
• 2002

A carboxydotrophic bacterium, isolated from a soil sample in Seoul, was classified initially as Acinetobacter sp. strain JC1 DSM 3803. Chemotaxanomic properties, analysis of the 16s rDNA sequence, fatty acid content, and molecular Phylogenetic analysis based on rpoB gene, however, suggested that this bacterium belongs to the genus, Mycobacterium. On the basis of this evidence, it is proposed that Acinetobacter sp. strain JC1 DSM 3803 be reclassified as Mycobacterium sp. strain JC1 DSM 3803.

• Journal of Microbiology and Biotechnology
• /
• v.13 no.4
• /
• pp.598-606
• /
• 2003

Salmonella encodes an enterotoxin (Stn) which possesses biological activity similar to the cholera toxin. Stn contributes significantly to the overall virulence of S. typhimurium in a murine model. The production of Stn is enhanced in a high-osmolarity medium and by contact with epithelial cells. In the present study, the in vitro and in vivo transcriptional regulations of the sin promoter revealed two promoters, P1 and P2. The P1 promoter identified by a primer extension analysis of stn mRNA exhibited a switching mechanism in vivo. Depending on the growth stage, transcription was initiated from different start sites termed $P1_S\;and\;P1_E$. $P1_S$, recognized by RNA polymerase containing ${\sigma}^S(E{\sigma}^S),\;and\;P1_E$, recognized by $E{\sigma}^70$, were activated during the stationary and exponential phases, respectively, while $P1_S\;and\;P1_E$ were both negatively regulated by CRPㆍcAMP and H-NS. Results revealed that $P1_S$ was the responsible promoter activated under a high osmolarity and low pH. The P2 promoter was identified 45 nucleotides downstream from $P1_E$ and negatively controlled by CRPㆍcAMP in vitro. No P2 activity was detected in vivo. The regulation of stn expression monitored using a Pstn::egfp fusion indicated that $E{\sigma}^S$ was required for the induction of stn and various factors were involved in stn regulation inside animal cells.

• Research in Plant Disease
• /
• v.24 no.2
• /
• pp.138-144
• /
• 2018

In December 2016, stem rot symptoms were observed on Persian buttercup (Ranunculus asiaticus) plants in Chilgok, Gyeongbuk, Korea. In the early stage of the disease, several black spots appeared on the stem of infected plants. As the disease progressed, the infected stem cleaved and wilted. The causal agent was isolated from a lesion and incubated on Reasoner's 2A (R2A) agar at $25^{\circ}C$. Total genomic DNA was extracted for phylogenetic analysis. Based on the 16S rRNA gene analysis, the isolated strain was found to belong to the genus Pseudomonas. To identify the isolated bacterial strain at the species level, the nucleotide sequences of the gyrase B (gyrB) and RNA polymerase D (rpoD) genes were obtained and compared with the sequences in the GenBank database. As the result, the causal agent of the stem rot disease was identified as Pseudomonas marginalis. To determine the pathogenicity of the isolated bacterial strain, it was inoculated into the stem of healthy R. asiaticus plant, the inoculated plant showed a lesion with the same characteristics as the naturally infected plant. Based on these results, this is the first report of bacterial stem rot on R. asiaticus caused by P. marginalis in Korea.

• Journal of Life Science
• /
• v.8 no.2
• /
• pp.216-225
• /
• 1998

Metal ion-induced and it’s regulatory genes were screened in virulent salmonella typhimurium UK1 and tested cross-regulation with various stresses. Using the techniqud of P22-MudJ(Km, lacZ)-directed lacZ operon fusion, LF40 cuiA::MudJ and Lf153 cuiD::MudJ which were induced by copper were selected. cuia and cuiD were determined anaerobic coper inducible and copper tolerance response gene, respectively. Also cuiA and cuiD locus were determined at 81 and 8min, respectively, on salmonella Genetic Map. The two regulators were identified as cuaR, and cudR, which controls cuiA and cuiD, respectively. cuaR, and cudR appeared as negative regulators because the expression of cuiA-lac-Z and cuiD-lacZ were increased. Copper adapted UK1 showed high resistance to H$_{2}$O$_{2}$, but cuiD did not. The product of the cudR locus was responsible for decreasing the tolerance to copper and H$_{2}$O$_{2}$. Furthemore cuiA and cuiD locus were found to be part of a regulon under the control of a trans-acting regulators, rpoS, oxyR and relA. Therefore, the results suggest CTR participate with oxidative stress on Salmonella.

• Research in Plant Disease
• /
• v.22 no.3
• /
• pp.158-167
• /
• 2016

A pathogen that causes a new disease on green pumpkin in the nursery and the field was characterized and identified. Symptoms of the disease on green pumpkin were water soaking lesions and spots with strong yellow halo on leaf, brown lesion on flower, and yellow spot on fruit. The bacterial isolates from the leaf spot were pathogenic on the 8 curcubitaceae crop plants, green pumpkin, figleaf gourd, wax gourd, young pumpkin, zucchini, cucumber, melon, and oriental melon, whereas they did not cause the disease on sweet pumpkin and watermelon. They were Gram-negative, rod shape with polar flagella, fluorescent on King's B agar and LOPAT group 1a by LOPAT test. Their Biolog substrate utilization patterns were similar to Pseudomonas syringae pv. syringae's in Biolog database. Phylogenetic trees with 16S rRNA gene sequences and multilocus sequence typing (MLST) with nucleotide sequences of 4 housekeeping genes, gapA, gltA, gyrB, rpoD and those of P. syringae complex strains in the Plant Associated and Environmental Microbes Database (PAMDB) showed that the green pumpkin isolates formed in the same clade with P. syringae pv. syringae strains. The clade in MLST tree was in the genomospecies 1 group. The phenotypic and genotypic characteristics suggested that the isolates from green pumpkin lesion were P. syringae pv. syringae.