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Complete genome sequence of Flavisolibacter ginsenosidimutans Gsoil 636T , a ginsenoside-converting bacterium, isolated from soil used for cultivating ginseng
Korean J. Microbiol. 2019;55(4):459-461
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Dong-Ho Keum1, Byoung Hee Lee2, Ki-Eun Lee2, Soon Youl Lee1, and Wan-Taek Im1,3*

1Department of Biotechnology, Hankyong National University, Gyeonggi-do 17579, Republic of Korea
2Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
3AceEMzyme Co., Ltd., Academic Industry Cooperation, Gyeonggi-do 17579, Republic of Korea
Correspondence to: *E-mail: wandra@hknu.ac.kr;
Tel.: +82-31-670-5335; Fax: +82-31-670-5339
Received October 30, 2019; Revised December 9, 2019; Accepted December 9, 2019.
Abstract

A yellow-colored, circular, convex, rod-shaped baterial strain designated Flavisolibacter ginsenosidimutans Gsoil 636T was isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea. Gsoil 636T showed the ability to convert Rb1 (one of the dominant active components of ginseng) to F2, and its whole genome was sequenced. The whole genome of Flavisolibacter ginsenosidimutans Gsoil 636T consist 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 636T, we identified several glycoside hydrolase-encoding genes that may be involved in the conversion of major ginsenosides into minor ginsenosides and unexpectedly found antibiotic biosynthesis-encoding genes and excinuclease genes.

Keywords : Flavisolibacter ginsenosidimutans, complete genome, ginseng soil, glycoside hydrolase, PacBio RS II
Body

The genus Flavisolibacter was first proposed by (Yoon and Im, 2007). Strain Gsoil 636T is 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 ginsengiterrae, 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 bacterium, Flavisolibacter ginsenosidimutans Gsoil 636T, 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 636T was 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 collections (= KCTC 22818T = JCM 18197T = KACC14277T).

Genomic DNA of F. ginsenosidimutans Gsoil 636T was 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 SMRTbellTM templates library, at DNA Link, Inc. Sequences were assembled using the HGAP3 (Pacific Biosciences) protocol 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, respectively.

The complete genome of F. ginsenosidimutans Gsoil 636T consisted 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 subunits, vitamin B12-dependent ribonucleotide reductase, multiple biosynthesis genes such as quinone biosynthesis C-methlylase (UbiE), the cellulose synthase (CesA), and bacillithiol biosynthesis 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.

General features of Flavisolibacter ginsenosidimutans Gsoil 636T

FeaturesChromosome
Genome size (bp)5,079,621
DNA coding region (bp)4,977,748
G + C content (%)48.9
Total genes4,338
Pseudo genes41
Protein-cording genes4,251
Number of rRNA genes (5S, 16S, 23S)3 (1, 1, 1)
Number of tRNA genes40
Number of ncRNA genes3

Nucleotide sequence accession number

The complete genome sequence of Flavisolibacter ginsenosidimutans Gsoil 636T has been deposited in DDBJ/EMBL/ NCBI GenBank under the accession number CP042433.

적 요

인삼 재배 토양으로부터 분리한 Flavisolibacter ginsenosidimutans Gsoil 636T 균주의 유전체서열을 분석하였다. 균주 Gsoil 636T는 진세노사이드 Rb1을 F2로 전환하는 능력을 보여주었다. Gsoil 636T의 유전체는 G + C 비율이 48.9%이며, 4,338개의 유전자와 4,251개의 단백질 코딩 유전자, 46개의RNA 유전자 그리고 41개의 위유전자를 포함한 단일 원형 염색체로 구성되었으며 그 크기는 5,079,612 bp였다. 전체 DNA 시컨싱을 통해 균주 Gsoil 636T이 여러 타입의 글라이코시다제 유전자를 가지고 있어 메이저 진세노사이드를 마이너진세노사이드로 전환하는 것을 확인하였다. 그 외에 항생제 생합성 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
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