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Complete genome sequence of Panacibacter ginsenosidivorans Gsoil 1550T , a ginsenoside-converting bacterium, isolated from soil of a ginseng field
Korean J. Microbiol. 2019;55(4):456-458
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 6, 2019; Accepted December 7, 2019.
Abstract

A yellow-colored, long rod baterial strain of low convexity, designated Panacibacter ginsenosidivorans Gsoil 1550T was isolated from soil of a ginseng field collected in Pocheon, Republic of Korea. Gsoil 1550T showed 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 1550T consisted 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 1550T, 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 B12-binding domain-containing genes.

Keywords : Panacibacter ginsenosidivorans, complete genome, ginseng soil, glycoside hydrolase, PacBio RS II
Body

The genus Panacibacter was first proposed by Sidiqqi et al. (2016). Gsoil 1550T is a ginsenoside-transforming, Gram-negative, non-motile, non-spore-forming, and long rod bacterium. It belongs 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 1550T was isolated from soil of a ginseng field in Republic of Korea. P. ginsenosidivorans Gsoil 1550T was 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 bioavailability, and better permeability across the cell membrane (Lei et al., 2016), strain P. ginsenosidivorans Gsoil 1550T was selected for a whole genome study to identify the target functional genes. This strain is available from two culture collections (= KCTC 12658T = JCM 31452T).

Genomic DNA of P. ginsenosidivorans Gsoil 1550T 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. (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 rRNAmmer and tRNAscan-SE, respectively.

The complete genome of P. ginsenosidivorans Gsoil 1550T consist 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 sequence 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-arabinofuranosidase, 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 antibiotic biosynthesis, and multiple antibiotic resistance proteins, antioxidant related genes like thiol-disulfide isomerase/thioredoxin, and cellulose synthase (CesA), excinuclease ABC subunit system genes (UvrA, UvrB, UvrC, and UvrD), and cobalamin B12-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.

General features of Panacibacter ginsenosidivorans Gsoil 1550T

FeaturesChromosome
Genome size (bp)5,528,026
DNA coding region (bp)5,466,112
G + C content (%)44.6
Total genes4,657
Pseudo genes33
Protein-cording genes4,572
Number of rRNA genes (5S, 16S, 23S)3 (1, 1, 1)
Number of tRNA genes46

Nucleotide sequence accession number

The complete genome sequence of Panacibacter ginsenosidivorans Gsoil 1550T has been deposited in DDBJ/EMBL/ NCBI GenBank under accession number CP042435.

적 요

한국 포천의 인삼 재배 토양으로부터 분리한 Panacibacter ginsenosidivorans Gsoil 1550T 균주의 유전체서열을 분석하였다. Panacibacter ginsenosidivorans Gsoil 1550T는 메이저 진세노사이드 Rb1, Rc 그리고 Rd를 마이너 진세노사이드 F2로 전환하는 능력을 보여주었다. 균주 Gsoil 1550T의 유전체는 G + C 비율이 44.6%이며, 4,657개의 유전자와 4,572개의 단백질 코딩 유전자, 52개의 RNA 유전자 그리고 33개의 위유전자를 포함한 단일 원형 염색체로 구성되었으며 그 크기는 5,528,026 bp였다. 균주 Gsoil 1550T는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자, 항생제 합성과 저항성 유전자와 비타민 B12 관련 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
  1. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, and Eichler EE, et al. 2013. Nonhybrid, finished microbial genome assemblies from longread SMRT sequencing data. Nat. Methods. 10, 563-569.
    Pubmed CrossRef
  2. Cui L, Wu SQ, Zhao CA, and Yin C. 2016. Microbial convertsion of major ginsenosides in ginseng total saponins by Platycodon grandiflorum endophytes. J. Ginseng. Res. 40, 366-374.
    Pubmed KoreaMed CrossRef
  3. DiCuccio M, Zaslavsky L, Chetvernin V, Ostell J, Badretdin A, Tatusova T, Lomsadze A, Borodovsky M, Nawrocki EP, and Pruitt KD. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef
  4. Kämpfer P, Lodders N, and Falsen E. 2011. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium,Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int. J. Syst. Evol. Microbiol. 61, 518-523.
    Pubmed CrossRef
  5. Roberts RJ, Carneiro MO, and Schatz MC. 2013. The advantages of SMRT sequencing. Genome Biol. 14, 405.
    Pubmed CrossRef
  6. Siddiqi MZ, Shafi SM, Choi KD, and Im WT. 2016. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol. 66, 4039-4045.
    Pubmed CrossRef


December 2019, 55 (4)