Korean Journal of Microbiology (2019) Vol. 55, No. 4, pp. 456-458 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2019.9134 eISSN 2383-9902
Copyright ⓒ 2019, The Microbiological Society of Korea
Complete genome sequence of Panacibacter ginsenosidivorans
Gsoil 1550 T , a ginsenoside-converting bacterium, isolated from soil of a ginseng field
Dong-Ho Keum
1, Byoung Hee Lee
2, Ki-Eun Lee
2, Soon Youl Lee
1, and Wan-Taek Im
1,3*
1
Department of Biotechnology, Hankyong National University, Gyeonggi-do 17579, Republic of Korea
2
Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
3
AceEMzyme Co., Ltd., Academic Industry Cooperation, Gyeonggi-do 17579, Republic of Korea
한국 인삼 밭 토양에서 분리한 진세노사이드 전환능력이 있는
Panacibacter ginsenosidivorans Gsoil 1550 T 의 유전체 서열 분석
금동호
1･ 이병희
2･ 이기은
2･ 이순열
1･ 임완택
1,3*
1
국립한경대학교 농업생명과학대학 생명공학과,
2국림생물자원관 미생물자원과,
3(주)에이스엠자임
(Received October 30, 2019; Revised December 6, 2019; Accepted December 7, 2019)
*For correspondence. E-mail: [email protected];
Tel.: +82-31-670-5335; Fax: +82-31-670-5339
A yellow-colored, long rod baterial strain of low convexity, designated Panacibacter ginsenosidivorans Gsoil 1550
Twas isolated from soil of a ginseng field collected in Pocheon, Republic of Korea. Gsoil 1550
Tshowed the ability to convert major ginsenosides Rb1, Rc, and Rd to minor ginsenoside F2, and its whole genome was sequenced. The whole genome sequence of Panacibacter ginsenosidivorans Gsoil 1550
Tcon- sisted of one circular chromosome of 5,528,026 bp, with 44.6%
G + C content. Of the 4,657 predicted genes, 4,572 were protein- cording genes, 52 were RNAs, and 33 were pseudogenes. From the complete genome sequence of the strain Gsoil 1550
T, we found several glycoside hydrolase-encoding genes that may be involved in the conversion of major ginsenosides into minor ginsenosides, antibiotic biosynthesis-encoding genes, and cobalamin B
12-binding domain-containing genes.
Keywords: Panacibacter ginsenosidivorans, complete genome, ginseng soil, glycoside hydrolase, PacBio RS II
The genus Panacibacter was first proposed by Sidiqqi et al.
(2016). Gsoil 1550
Tis a ginsenoside-transforming, Gram-negative, non-motile, non-spore-forming, and long rod bacterium. It be- longs to the family Chitinophagaceae which was first proposed by Kämpfer et al. (2011) within the phylum Bacteroidetes.
Members of Chitinophagaceae are usually non-motile, aerobic or facultatively anaerobic with cells that are often thin rod- shaped.
To identify a ginsenoside transforming-positive bacterium, the Gram-negative Panacibacter ginsenosidivorans Gsoil 1550
Twas isolated from soil of a ginseng field in Republic of Korea.
P. ginsenosidivorans Gsoil 1550
Twas yellow-pigment, non- motile and long rod-shaped. To investigate the genes involved in production of minor ginsenosides from major ginsenosides.
Minor ginsenosides (Rh1, Rh2, F2, Rg3, C-K, etc.) are more
pharmaceutically active than major ginsenosides (Rb1, Rb2,
Rc, Rd, Rg1, etc.), because of their smaller size, higher bio-
availability, and better permeability across the cell membrane
(Lei et al., 2016), strain P. ginsenosidivorans Gsoil 1550
Twas
selected for a whole genome study to identify the target
functional genes. This strain is available from two culture
Complete genome sequence of P. ginsenosidivorans Gsoil 1550
T∙ 457
Korean Journal of Microbiology, Vol. 55, No. 4 Table 1. General features of Panacibacter ginsenosidivorans Gsoil 1550
TFeatures Chromosome
Genome size (bp) 5,528,026
DNA coding region (bp) 5,466,112
G + C content (%) 44.6
Total genes 4,657
Pseudo genes 33
Protein-cording genes 4,572
Number of rRNA genes (5S, 16S, 23S) 3 (1, 1, 1)
Number of tRNA genes 46
collections (= KCTC 12658
T= JCM 31452
T).
Genomic DNA of P. ginsenosidivorans Gsoil 1550
Twas extracted using a MagAttract HMW DNA kit (Qiagen) and was purified using the chloroform wash method (shared protocol;
Pacific Biosciences). Genome sequencing was performed using a Pacific Biosciences RSII sequencing platform, with a 20 kb SMRTbell
TMtemplates library, at DNA Link, Inc. (Roberts et al., 2013). Sequences were assembled using the HGAP3 (Pacific Biosciences) protocol and the sequencing depth was 141.34×
(Chin et al., 2013). The genome sequence was annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/books/NBK174280/) (DiCuccio et al., 2016). rRNAs and tRNAs were predicted using rRN- Ammer and tRNAscan-SE, respectively.
The complete genome of P. ginsenosidivorans Gsoil 1550
Tconsist of one circular chromosome of 5,528,026 bp, with 44.6% G + C content. Of the 4,657 predicted genes, 4,572 were protein-cording genes (CDSs with protein), 52 were RNAs, and 33 were pseudogenes. The majority of the protein coding genes (98.88%) was assigned function, while the remaining predicted in Table 1. Analysis of the complete genome se- quence showed more than 30 glycoside hydrolase-encoding genes that may be involved in the conversion of ginsenosides including β-glucosidase, α-glucosidase, β-xylosidase, α-ara- binofuranosidase, α-L-rhamnosidase, and β-galactosidase. In addition, genome annotation revealed other genes of interest, including nitrite reductase, large subunit, polysaccharide lyases such as β-glucanase, antibiotic related genes, such as bleomycin resistance protein, monooxygenase genes associated with anti- biotic biosynthesis, and multiple antibiotic resistance proteins, antioxidant related genes like thiol-disulfide isomerase/thiore- doxin, and cellulose synthase (CesA), excinuclease ABC subunit
system genes (UvrA, UvrB, UvrC, and UvrD), and cobalamin B
12-binding domain-containing protein. Although we not check the function of the genes, they maybe has potential ability and the presence of these genes supports the importance of the bacterial type represented by this strain for the cycling of organic and inorganic elements.
Nucleotide sequence accession number
The complete genome sequence of Panacibacter ginseno- sidivorans Gsoil 1550
Thas been deposited in DDBJ/EMBL/
NCBI GenBank under accession number CP042435.
적 요
한국 포천의 인삼 재배 토양으로부터 분리한 Panacibacter ginsenosidivorans Gsoil 1550
T균주의 유전체서열을 분석하 였다. Panacibacter ginsenosidivorans Gsoil 1550
T는 메이저 진세노사이드 Rb1, Rc 그리고 Rd를 마이너 진세노사이드 F2 로 전환하는 능력을 보여주었다. 균주 Gsoil 1550
T의 유전체 는 G + C 비율이 44.6%이며, 4,657개의 유전자와 4,572개의 단백질 코딩 유전자, 52개의 RNA 유전자 그리고 33개의 위유 전자를 포함한 단일 원형 염색체로 구성되었으며 그 크기는 5,528,026 bp였다. 균주 Gsoil 1550
T는 인삼사포닌의 당 분해 에 관여하는 여러 타입의 글라이코시다제 유전자, 항생제 합성
과 저항성 유전자와 비타민 B
12관련 유전자를 가지고 있었다.
Acknowledgements
This work was supported by grants from the National Institute of Biological Resources, funded by the Ministry of Environment (No.NIBR201801106).
References
