Korean Journal of Microbiology (2019) Vol. 55, No. 4, pp. 454-455 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2019.9133 eISSN 2383-9902
Copyright ⓒ 2019, The Microbiological Society of Korea
Complete genome sequence of Arachidicoccus ginsenosidivorans Gsoil 809 T , a ginsenoside-converting bacterium, isolated from ginseng cultivating soil
Ji Eun Lee
1, Byoung Hee Lee
2, Ki-Eun Lee
2, Myung-Suk Kang
2, 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
인삼토양으로부터 분리한 진세노사이드 전환 능력이 있는
Arachidicoccus ginsenosidivorans Gsoil 809 T 의 유전체 서열 분석
이지은
1･ 이병희
2･ 이기은
2･ 강명석
2･ 임완택
1,3*
1
국립한경대학교 농업생명과학대학 생명공학과,
2국립생물자원관 미생물자원과,
3㈜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 Gram-stain-negative, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium, designated Arachidicoccus ginse- nosidivorans Gsoil 809
T, was isolated from soil of a ginseng field. Arachidicoccus ginsenosidivorans Gsoil 809
Tshowed the ability to transform major ginsenoside Rg1 to minor gin- senoside Rh1, and its whole genome was sequenced. The whole genome of Arachidicoccus ginsenosidivorans Gsoil 809
Tconsists of a single circular chromosome of 5,773,153 bp, with 41.1% G + C content. Based on the complete genome sequence of strain Gsoil 809
T, we found several glycoside hydrolase- encoding genes and polysaccharide lyases.
Keywords: Arachidicoccus ginsenosidivorans, complete genome, glycoside hydrolase, PacBio RS II, soil of ginseng field
The genus Arachidicoccus was recently described by Mad- haiyan et al. (2015). Species of this genus were Gram-stain- negative, non-motile, non-sporeforming, coccoid rods and formed non-pigmented colonies. The DNA G + C content
ranges between 43.1 and 44.3%. Currently, the genus com- prises of 2 recognized species with published names (LPSN, http://www.bacterio.net/niabella.html), which are commonly isolated from rhizosphere soils.
A Gram-stain-negative bacterium, Arachidicoccus ginseno- sidivorans Gsoil 809
T, was isolated from ginseng cultivating soil, in the Republic of Korea. A. ginsenosidivorans Gsoil 809
Twas light yellow coloured, non-spore-forming, non-motile, and rod-shaped bacterium. Based on the production of minor ginsenoside Rh1 from major ginsenoside Rg1 (Siddiqi et al., 2017), Gsoil 809
Twas selected for a whole genome study to identify the target functional genes. Whole genome sequence analysis showed many glycoside hydrolases that may be involved in the conversion of ginsenosides. This strain is available from the host institute and from two culture col- lections (= KCTC 22820
T= JCM30984
T).
Genomic DNA of A. ginsenosidivorans Gsoil 809
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
Complete genome sequence of A. ginsenosidivorans Gsoil 809
T∙ 455
Korean Journal of Microbiology, Vol. 55, No. 4 Table 1. General features of Arachidicoccus ginsenosidivorans Gsoil 809
TFeatures Chromosome
Genome size (bp) 5,773,153
G + C content (%) 41.1%
Total genes 4,628
Pseudo genes 496
Coding sequences (CDSs) 4,073
Number of rRNA genes (5S, 16S, 23S) 9 (3, 3, 3)
Number of tRNA genes 47
a Pacific Biosciences RSII sequencing platform, with a 20 kb SMRTbell
TMtemplate library, at DNA Link, Inc. Sequences were assembled using the HGAP3 protocol (Pacific Bio- sciences) and the sequencing depth was 60.58 ×. The genome sequence was annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/
books/NBK174280/). rRNAs and tRNAs were predicted using rRNAmmer and tRNAscan-SE, respectively (Anthony and Kin, 2015).
The complete genome of A. ginsenosidivorans Gsoil 809
Tconsist of one circular chromosome of 5,773,153 bp, with 41.1% G + C content. Of the 4,628 predicted genes, 4,073 were protein-coding genes (CDS), and 59 were RNA genes. More- over, 496 pseudogenes were also identified. The majority of the protein-coding genes (89.14%) were assigned a putative func- tion. The genome statistics are presented in Table 1. Whole genome sequence analysis showed more than 96 hydrolase- encoding genes, including 18 β-glucosidases, 21 α-glucosidases, 41 β-xylosidases, 7 α-L-rhamnosidases, and 3 β-galactosidases which may be responsible for its ability to convert ginseno- sides. In addition, genome annotation revealed other genes of interest, including polysaccharide lyases such as α-amylase and cellulase, antibiotic bleomycin resistance, nitrite reductase, photosynthetic reaction center cytochrome c subunit gene which may synthesize organic matter on its own, photolyase which may repair the DNA caused by exposure to ultraviolet light (Junpei et al., 2017). The being of these genes show the significance for the cycling of organic and inorganic elements.
Nucleotide sequence accession number
The complete genome sequence of Arachidicoccus ginseno- sidivorans Gsoil 809
Thas been deposited in NCBI GenBank
under accession number CP042434.
적 요
인삼토양으로부터 분리한 Arachidicoccus ginsenosidivorans Gsoil 809
T균주의 유전체서열을 분석하였다. 균주 Gsoil 809
T의 유전체는 G + C 비율이 41.1%이며 4,628개의 유전자와 4,073개의 단백질 코딩 유전자, 496개의 위유전자 그리고 59 개의 RNA 유전자를 포함한 단일 원형 염색체로 구성되었으 며 그 크기는 5,773,153 bp였다. Gsoil 809
T는 주요 진세노사이 드 Rg1을 마이너 진세노사이드 Rh1로 변환하는 능력을 보여 주었다. Gsoil 809
T는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자, 고분자 분해 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
