Korean Journal of Microbiology (2019) Vol. 55, No. 4, pp. 459-461 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2019.9131 eISSN 2383-9902
Copyright ⓒ 2019, The Microbiological Society of Korea
Complete genome sequence of Flavisolibacter ginsenosidimutans Gsoil 636 T , a ginsenoside-converting bacterium, isolated from soil used for cultivating ginseng
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
인삼 재배 토양에서 분리한 진세노사이드 전환능력이 있는
Flavisolibacter ginsenosidimutans Gsoil 636 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 9, 2019; Accepted December 9, 2019)
*For correspondence. E-mail: [email protected];
Tel.: +82-31-670-5335; Fax: +82-31-670-5339
A yellow-colored, circular, convex, rod-shaped baterial strain designated Flavisolibacter ginsenosidimutans Gsoil 636
Twas isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea. Gsoil 636
Tshowed the ability to con- vert Rb1 (one of the dominant active components of ginseng) to F2, and its whole genome was sequenced. The whole genome of Flavisolibacter ginsenosidimutans Gsoil 636
Tconsist of a single circular chromosome of 5,079,621 bp, with 48.9% G + C content. Of the 4,338 predicted genes, 4,251 were protein- cording genes, 46 were RNAs, and 41 were pseudogenes. Using the complete genome sequence of the strain Gsoil 636
T, we identified several glycoside hydrolase-encoding genes that may be involved in the conversion of major ginsenosides into minor ginsenosides and unexpectedly found antibiotic bio- synthesis-encoding genes and excinuclease genes.
Keywords: Flavisolibacter ginsenosidimutans, complete genome, ginseng soil, glycoside hydrolase, PacBio RS II
The genus Flavisolibacter was first proposed by (Yoon and
Im, 2007). Strain Gsoil 636
Tis Gram-negative-bacterium, rod- shaped, non-motile, non-spore-forming, yellow-pigmented and is allocated to the family Chitinophagaceae. Within the genus Flavisolibacter, the genomic DNA G + C content range is from 42.7 to 46.4 mol%. Based on recent studies, this genus consists of four species with validly published names and isolated from various sources such as soil and water: Flavisolibacter gin- sengiterrae, Flavisolibacter ginsengisoli (Yoon and Im, 2007), Flavisolibacter rigui (Baik et al., 2014), and Flavisolibacter tropicus (Lee et al., 2016).
A ginsenoside transforming-positive, Gram-negative bacte- rium, Flavisolibacter ginsenosidimutans Gsoil 636
T, were isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea. Based on the transform from major ginsenosides to minor ginsenosides (Zhao et al., 2015), F.
ginsenosidimutans Gsoil 636
Twas chosed for a whole genome
study to identify the target functional genes. Whole genome
sequence analysis showed more than 70 glycoside hydrolases
that could be involved in the conversion of ginsenosides. This
strain is available from the host institute and from three culture
460 ∙ Keum et al.
미생물학회지 제55권 제4호
Table 1. General features of Flavisolibacter ginsenosidimutans Gsoil 636
TFeatures Chromosome
Genome size (bp) 5,079,621
DNA coding region (bp) 4,977,748
G + C content (%) 48.9
Total genes 4,338
Pseudo genes 41
Protein-cording genes 4,251
Number of rRNA genes (5S, 16S, 23S) 3 (1, 1, 1)
Number of tRNA genes 40
Number of ncRNA genes 3
collections (= KCTC 22818
T= JCM 18197
T= KACC14277
T).
Genomic DNA of F. ginsenosidimutans Gsoil 636
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. Sequences were assembled using the HGAP3 (Pacific Biosciences) pro- tocol and the sequencing depth was 194.66×. 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 rRNAmmer and tRNAscan-SE, respec- tively.
The complete genome of F. ginsenosidimutans Gsoil 636
Tconsisted of one circular chromosome of 5,079,621 bp, with 48.9% G + C content. Of the 4,338 predicted genes, 4,251 were protein-cording genes (CDSs), and 46 were RNA genes, and 41 pseudogenes. The majority of the protein coding genes (99.04%) was assigned function, while the remaining predicted in Table 1. Analysis of the complete genome sequence showed many glycoside hydrolase-encoding genes, including 10 β-glucosidases, 8 α-glucosidases, 23 β-xylosidases, 3 α-arabinofuranosidases, and 32 β-galactosidases, which may be related for its ability to convert ginsenosides. In addition, genome annotation revealed other genes of interest, including nitrite reductase large sub- units, vitamin B
12-dependent ribonucleotide reductase, multiple biosynthesis genes such as quinone biosynthesis C-methlylase (UbiE), the cellulose synthase (CesA), and bacillithiol bio- synthesis deacetylase (BshB1), antibiotic related genes such as bleomycin resistance proteins, monooxygenase genes associated
with antibiotic biosynthesis, and multiple antibiotic resistance proteins, excision endonuclease such as UvrABC subunits.
Nucleotide sequence accession number
The complete genome sequence of Flavisolibacter ginseno- sidimutans Gsoil 636
Thas been deposited in DDBJ/EMBL/
NCBI GenBank under the accession number CP042433.
적 요
인삼 재배 토양으로부터 분리한 Flavisolibacter ginseno- sidimutans Gsoil 636
T균주의 유전체서열을 분석하였다. 균주 Gsoil 636
T는 진세노사이드 Rb1을 F2로 전환하는 능력을 보 여주었다. Gsoil 636
T의 유전체는 G + C 비율이 48.9%이며, 4,338개의 유전자와 4,251개의 단백질 코딩 유전자, 46개의
RNA 유전자 그리고 41개의 위유전자를 포함한 단일 원형 염
색체로 구성되었으며 그 크기는 5,079,612 bp였다. 전체 DNA 시컨싱을 통해 균주 Gsoil 636
T이 여러 타입의 글라이코시다 제 유전자를 가지고 있어 메이저 진세노사이드를 마이너진세 노사이드로 전환하는 것을 확인하였다. 그 외에 항생제 생합 성 유전자와 UV 관련 유전자도 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
