Draft Genome Analysis of Antimicrobial Streptomyces Isolated from Himalayan Lichen

( Byeollee Kim ),( So-ra Han ),( Janardan Lamichhane ),( Hyun Park ),( Tae-jin Oh ) 한국미생물·생명공학회 2019 Journal of microbiology and biotechnology Vol.29 No.7

There have been several studies regarding lichen-associated bacteria obtained from diverse environments. Our screening process identified 49 bacterial species in two lichens from the Himalayas: 17 species of Actinobacteria, 19 species of Firmicutes, and 13 species of Proteobacteria. We discovered five types of strong antimicrobial agent-producing bacteria. Although some strains exhibited weak antimicrobial activity, NP088, NP131, NP132, NP134, and NP160 exhibited strong antimicrobial activity against all multidrug-resistant strains. Polyketide synthase (PKS) fingerprinting revealed results for 69 of 148 strains; these had similar genes, such as fatty acid-related PKS, adenylation domain genes, PfaA, and PksD. Although the association between antimicrobial activity and the PKS fingerprinting results is poorly resolved, NP160 had six types of PKS fingerprinting genes, as well as strong antimicrobial activity. Therefore, we sequenced the draft genome of strain NP160, and predicted its secondary metabolism using antiSMASH version 4.2. NP160 had 46 clusters and was predicted to produce similar secondary metabolites with similarities of 5-100%. Although NP160 had 100% similarity with the alkylresorcinol biosynthetic gene cluster, our results showed low similarity with existing members of this biosynthetic gene cluster, and most have not yet been revealed. In conclusion, we expect that lichen-associated bacteria from the Himalayas can produce new secondary metabolites, and we found several secondary metabolite-related biosynthetic gene clusters to support this hypothesis.

Complete genome sequencing of <i>Shigella</i> sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation

Han, So-Ra,Kim, Do Wan,Kim, Byeollee,Chi, Young Min,Kang, Seunghyun,Park, Hyun,Jung, Sang-Hee,Lee, Jun Hyuck,Oh, Tae-Jin Elsevier 2019 Microbial pathogenesis Vol.137 No.-

<P><B>Abstract</B></P> <P> <I>Shigella</I> sp. PAMC 28760 (isolated from <I>Himantormia</I> sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated <I>S.</I> sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus <I>Shigella</I>, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. <I>S.</I> sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding <I>Shigella</I> survival adaptation mechanisms under extremely cold Antarctic conditions.</P> <P><B>Highlights</B></P> <P> <UL> <LI> <I>Shigella</I> sp. PAMC 28760 from an Antarctic lichen has cellulolytic, amylolytic, and glycogen metabolic pathway. </LI> <LI> The complete genome of <I>Shigella</I> sp. PAMC 28760 showing differences from pathogenic reported previously. </LI> <LI> The foundation for understanding <I>Shigella</I> adaptation mechanism to extremely conditions is provided. </LI> </UL> </P>

Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species

Gupta Sushma,Han So-Ra,Kim Byeollee,Lee Chang-Muk,Oh Tae-Jin 한국유전학회 2022 Genes & Genomics Vol.44 No.6

Background: The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available. Objective: The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation. Methods: Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle. Results: Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. Conclusions: The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.

Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach

So‑Ra Han,Sung‑Min Jang,Young Min Chi,Byeollee Kim,정상희,Yung Mi Lee,Jun Uetake,Jun Hyuck Lee,Hyun Park,오태진 한국유전학회 2020 Genes & Genomics Vol.42 No.9

Background Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. Objective In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region. Methods Genome sequencingwas performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI nonredundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes). Results The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confrmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway. Conclusion In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by fnding new genes that degradation the pectin