https://repository.kopri.re.kr/handle/201206/9724 2026-04-21T12:54:54Z https://repository.kopri.re.kr/handle/201206/10891 Title: Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome Authors: Shin, Seung Chul; Kim, Hyun; Lee, Jun Hyuck; Kim, Han-Woo; Park, Joonho; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Ji Hee; Lee, Hyoungseok; Kim, Sanghee Abstract: Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly and the annotated gene sets. Recently, assembly contiguity has been increased using nanopore technology. A number of methods for enhancing the low base quality of the assembly have been reported, including long-read (e.g. Nanopolish) or short-read (e.g. Pilon) based methods. Based on these advances, we used nanopore technologies to upgrade the draft genome sequence of P. steinenii. The final assembled genome was 145,366,448 bases in length. The contig number decreased from 9,132 to 162, and the N50 contig size increased from 36,946 to 1,989,550 bases. The BUSCO completeness of the assembly increased from 87.8 to 98.7%. Improved assembly statistics helped predict more genes from the draft genome of P. steinenii. The completeness of the predicted gene model increased from 79.5 to 92.1%, but the numbers and types of the predicted repeats were similar to those observed in the short read assembly, with the exception of long interspersed nuclear elements. In the present study, we markedly improved the P. steinenii genome assembly statistics using nanopore sequencing, but found that genome polishing with high-quality reads was essential for improving genome annotation. The number of genes predicted and the lengths of the genes were greater than before, and nanopore technology readily improved genome information. 2019-03-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/9664 Title: Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp. Authors: Park, Sun-Ha; Lee, Jun Hyuck; Kim, T. Doohun; Kim, Kyeong Kyu; Park, Hyun; Kim, Han-Woo; Shin, Seung Chul; Jeong, Chang Sook; Lee, Chang Woo; Yoo, Wanki Abstract: Cold-active acetyl xylan esterases allow for reduced bioreactor heating costs in bioenergy production. Here, we isolated and characterized a cold-active acetyl xylan esterase (PbAcE) from the psychrophilic soil microbe Paenibacillus sp. R4. The enzyme reversibly hydrolyzes glucose penta-acetate and xylan acetate, alternatively producing acetyl xylan from xylan, and it shows higher activity at 4°C than at 25°C. We solved the crystal structure of PbAcE at 2.1-A resolution to investigate its active site and the reason for its low-temperature activity. Structural analysis showed that PbAcE forms a hexamer with a central substrate binding tunnel, and the inter-subunit interactions are relatively weak compared with those of its mesophilic and thermophilic homologs. PbAcE also has a shorter loop and different residue composition in the β4？α3 and β5？α4 regions near the substrate binding site. Flexible subunit movements and different active site loop conformations may enable the strong low-temperature activity and broad substrate specificity of PbAcE. In addition, PbAcE was found to have strong activity against antibiotic compound substrates, such as cefotaxime and 7-amino cephalosporanic acid (7-ACA). In conclusion, the PbAcE structure and our biochemical results provide the first example of a cold-active acetyl xylan esterase and a starting template for structure-based protein engineering. 2018-10-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/10857 Title: Complete genome sequence of Colwellia hornerae PAMC 20917, a cold-active enzyme-producing bacterium isolated from the Arctic Ocean sediment Authors: Kim, Hyun; Park, Ae Kyung; Lee, Jun Hyuck; Kim, Han-Woo; Shin, Seung Chul Abstract: Psychrophilic bacteria are considered a source of cold-active enzymes that can be used in industrial applications.The Arctic bacterium Colwellia hornerae PAMC 20917 strain has been isolated from the o？shore sediment nearNy-Alesund, Svalbard. The optimal growth temperature of the strain was 10 °C on marine agar. The cell lysateshowed alkaline phosphatase activities. Analysis of the enzymatic properties showed that the alkaline phos-phatase was cold-active and thermolabile. To explore useful cold-active industrial enzymes further, the entiregenome of the PAMC 20917 strain was sequenced. The genome of the strain contained 4,684,314 nucleotides,with 37.87% G+C content. Genome mining analysis revealed that, in the complete genome sequence, threeproteins were annotated as alkaline phosphatases. The genome of PAMC 20917 encodes cold shock proteins andan ice-binding protein that inhibits the growth of ice, allowing the bacterium to adapt to cold environments. Thisgenome information may be useful for understanding mechanisms of adaptation to cold stress. 북극해양침전물로 부터 분리한 Colwellia hornerae PAMC 20917의 유전체 해독 논문: Colwellia의 경우 해양 미생물로서 저온 효소를 많이 가지고 있는 것으로 알려져 있다. 이균주로 부터 저온 알칼라인 포스파타아제를 분비하는 것을 확인하고 유전정보를 확보하기 위해서 유전체 분석을 수행하였다. 3개의 알칼라인 포스파타아제를 유전체에서 확인하였으며, 추가적인 저온 효소로 가치가 있는 아밀라아제, 프로테아제, 글루카나아제 및 풀루란나아제 등을 확인할 수 있었으며, 추가적인 연구로 산업적인 적용에 대해서 고려해 볼 수 있을 것 같다. 2018-10-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/10525 Title: PsEst3, a new psychrophilic esterase from the Arctic bacterium Paenibacillus sp. R4: crystallization and X-ray crystallographic analysis Authors: Kim, Hyun; Park, Ae Kyung; Lee, Jun Hyuck; Shin, Seung Chul; Park, Hyun; Kim, Han-Woo Abstract: Esterases are very useful biocatalysts in industry: they hydrolyze esters and split them into a carboxylic acid and an alcohol. The psychrophilic esterase PsEst3 was obtained from Paenibacillus sp. R4, which was isolated from the active layer of the permafrost in Council, Alaska. PsEst3 was successfully overexpressed using a psychrophilic chaperonin co-expression system and was purified by nickel-affinity and size-exclusion chromatography. Recombinant PsEst3 was crystallized at 290 K using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 A ° resolution. The crystal was determined to belong to space group P4132 or P4332, with unit-cell parameters a = b = c = 145.33 A ° . Further crystallographic analysis needs to be conducted to investigate the structure and function of this esterase. 2018-06-01T00:00:00Z