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Complete genome sequence of Nibribacter radioresistens DG15C, a radiation resistant bacterium
Gayathri Sathiyaraj,Myung Kyum Kim,Ju-Young Kim,Su Jeong Kim,장준휘,Soohyun Maeng,Myung-Suk Kang,Sathiyaraj Srinivasan 대한독성 유전단백체 학회 2018 Molecular & cellular toxicology Vol.14 No.3
Backgrounds: The ionizing radiation from the gamma rays is damaging the genetic materials of the cells, possibly leading to cell death and cause permanent changes within daughter cells. A red pigmented, Gramnegative, aerobic, short-rod shaped, non-motile, UV and gamma radiation tolerant bacterium Nibribacter radioresistens DG15C was isolated from a soil sample collected in a rice field in South Korea. Methods: The complete genome of DG15C was sequenced and assembled using Pacific Biosciences RS II system. The genome sequence was annotated using Genomes-Expert Review (IMG-ER) platform, Prodigal, and JGI GenePRIMP pipeline. The protein-coding genes were identified using Prodigal, Pfam and COG databases implemented in the IMG systems. Results: The complete genome sequence of strain DG15C consists of a circular chromosome (4,143,738 bp) encoding 3,969 coding sequences (CDs) and 3,582 genes. The bacterium showed resistance to gamma and UVC radiations. Conclusion: The genome annotation as confirmed the presence of gene clusters involved in the toxicity resistance of radiation.
Sathiyaraj, Gayathri,Srinivasan, Sathiyaraj,Kim, Ho-Bin,Subramaniyam, Sathiyamoorthy,Lee, Ok Ran,Kim, Yeon-Ju,Yang, Deok Chun Sociedade Brasileira de Microbiologia 2011 Brazilian journal of microbiology Vol.42 No.2
<P><I>Cylindrocarpon destructans</I> isolated from ginseng field was found to produce pectinolytic enzymes. A Taguchi’s orthogonal array experimental design was applied to optimize the preliminary production of polygalacturonase (PG) and pectin lyase (PL) using submerged culture condition. This method was applied to evaluate the significant parameters for the production of enzymes. The process variables were pH, pectin concentration, incubation time and temperature. Optimization of process parameters resulted in high levels of enzyme (PG and PL) production after ten days of incubation at a pH of 5.0 at 25°C in the presence of 1.5% pectin. Among different nitrogen sources, urea and peptone showed high production of PG and PL, respectively. The enzyme production and mycelial growth seems to have direct influence on the culture conditions; therefore, at stationary state high enzyme production and mycelial growth were obtained than agitation state. Along with this, optimization of enzyme activity was also determined using various physiological parameters like, temperature, incubation time and pH. Taguchi’s data was also analyzed using one step ANOVA statistical method.</P>
Complete genome sequence of Microvirga sp. 17mud 1-3, a radiation-resistant bacterium
Gayathri Sathiyaraj,Myung Kyum Kim,Ju-Young Kim,Su Jeong Kim,장준휘,Soohyun Maeng,Myung-Suk Kang,Sathiyaraj Srinivasan 대한독성 유전단백체 학회 2018 Molecular & cellular toxicology Vol.14 No.3
Backgrounds: The genera Deinococcus Hymenobacter, Spirosoma, and Rubrobacter are renowned as an extremophilic bacteria. Most of the species of these genera have been shown to be either gamma radiation resistant or UV radiation resistant or both. Strain 17mud 1-3 was isolated from gamma-irradiated mud sample collected at Boryeong beach, South Korea. Methods: The genome of strain 17mud 1-3 was sequenced and assembled using Pacific Biosciences RS II system. The genome sequence was annotated using Genomes-Expert Review (IMG-ER) platform, Prodigal, and JGI GenePRIMP pipeline. The protein-coding genes were identified using Prodigal, Pfam and COG databases implemented in the IMG systems. Results: The complete genome consists of a circular chromosome (4,403,107 bp) encoding 4,368 coding sequences (CDs) and 4,301genes. Conclusion: The new strains showed both gamma and UV-C irradiation resistance and their complete genome sequence annotation features showed the presence of the genes involved in the radiation-resistance.
Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field
Srinivasan, Sathiyaraj,Kim, Myung Kyum,Sathiyaraj, Gayathri,Kim, Yeon-Ju,Yang, Deok-Chun Microbiology Society 2010 International journal of systematic and evolutiona Vol.60 No.8
<P>Two novel strains of Gram-negative, non-sporulating, short rod-shaped, motile bacteria, designated DCY25<SUP>T</SUP> and DCY28, were isolated from soil of a ginseng field in South Korea and characterized in order to determine their taxonomic position. 16S rRNA gene sequence analysis showed that strains DCY25<SUP>T</SUP> and DCY28 belonged to the <I>Betaproteobacteria</I>, the highest sequence similarities being found with <I>Pusillimonas noertemannii</I> BN9<SUP>T</SUP> (96.9 %), <I>Bordetella trematum</I> DSM 11334<SUP>T</SUP> (95.9 %), <I>Achromobacter denitrificans</I> DSM 30026<SUP>T</SUP> (95.9 %), <I>Achromobacter insolitus</I> LMG 6003<SUP>T</SUP> (95.8 %) and <I>Pigmentiphaga kullae</I> K24<SUP>T</SUP> (95.5 %). Chemotaxonomic data revealed that both strains DCY25<SUP>T</SUP> and DCY28 possessed ubiquinone Q-8. Fatty acid analysis of strain DCY25<SUP>T</SUP> demonstrated the presence of 19 : 0 cyclo <I>ω</I>8<I>c</I> (22.8 %) and 16 : 0 (16.6 %). The polar lipid profiles of strains DCY25<SUP>T</SUP> and DCY28 included phosphatidylethanolamine, phosphatidylglycerol, two unknown aminolipids and diphosphatidylglycerol. The G+C contents of strains DCY25<SUP>T</SUP> and DCY28 were 57.3 and 57.2 mol%, respectively. DNA-DNA relatedness values, biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strains DCY25<SUP>T</SUP> and DCY28 from <I>Pusillimonas noertemannii</I>. Therefore, strains DCY25<SUP>T</SUP> and DCY28 should be classified in a novel species, for which the name <I>Pusillimonas ginsengisoli</I> sp. nov. is proposed. The type strain is DCY25<SUP>T</SUP> (=KCTC 22046<SUP>T</SUP> =JCM 14767<SUP>T</SUP>); strain DCY28 (=KCTC 22047=JCM 14768) is a reference strain.</P>