search for




 

Complete genome sequence of Anseongella ginsenosidimutans Gsoil 524T , a ginsenoside-converting bacterium, isolated from soil cultivating ginseng
Korean J. Microbiol. 2019;55(4):451-453
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Ji Eun Lee1, Byoung Hee Lee2, Ki-Eun Lee2, Myung-Suk Kang2, 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 Gram-stain-negative, rod-shaped, non-spore-forming, aerobic bacterium, designated Anseongella ginsenosidimutans Gsoil 524T, was isolated from the soil of a field used for cultivating ginseng. Anseongella ginsenosidimutans Gsoil 524T showed the ability to convert major ginsenosides to minor ginsenosides, and its whole genome was sequenced. The whole genome of Anseongella ginsenosidimutans Gsoil 524T consists of a single circular chromosome of 4,322,684 bp, with 49.9% G + C content. Based on the complete genome sequence of strain Gsoil 524T, we found several glycoside hydrolase-encoding genes that may be involved in the conversion of major ginsenosides into minor ginsenosides and some polysaccharide lyases.

Keywords : Anseongella ginsenosidimutans, complete genome, glycoside hydrolase, PacBio RS II, the soil of ginseng field
Body

Based on the 16S rRNA gene sequence, Anseongellaginsenosidimutans Gsoil 524T in a distinct lineage in the family Sphingobacteriaceae which was first proposed by Steyn et al. (1998), belongs to the phylum Bacteroidetes, class Sphingobacteriia, and order Sphingobacteriales.

Anseongellaginsenosidimutans Gsoil 524T is Gram-stain-negative, rod-shaped, and non-spore-forming that is isolated from soil (Siddiqi et al., 2016). Currently, the genus comprises one recognized species with published names (LPSN, http://www.bacterio.net/niabella.html).

A Gram-strain-negative bacterium, A. ginsenosidimutans Gsoil 524T, were isolated from soil of a ginseng field in the Republic of Korea. A. ginsenosidimutans Gsoil 524T was milky-white colored, non-spore forming, and non-motile rod bacterium. Based on the production of minor ginsenosides from major ginsenosides (Siddiqi et al., 2017). A. ginsenosidimutans Gsoil 524T was selected for a whole genome study to identify the target functional genes such as glycoside hydrolases and polysaccharide lyases. 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 three culture collections (= KACC 14636T = KCTC 22261T = LMG 24494T).

Genomic DNA of A. ginsenosidimutans Gsoil 524T 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 template library, at DNA Link, Inc. Sequences were assembled using the HGAP3 protocol (Pacific Biosciences) and the sequencing depth was 173.03×. 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. ginsenosidimutans Gsoil 524T consists of one circular chromosome of 4,322,684 bp, with 49.9% G + C content. Of the 3,683 predicted genes, 3,448 were protein-coding genes (CDS), and 58 were RNA genes. Moreover, 177 pseudogenes were identified. The majority of the protein-coding genes (95.12%) was assigned function genes, while the remaining predicted genes were annotated as hypothetical or conserved hypothetical proteins. The genome statistics are presented in Table 1. Whole genome sequence analysis showed more than 20 hydrolase-encoding genes, including 2 β-glucosidases, 2 α-glucosidases, 13 β-xylosidases, 2 α-L-arabinofuranosidases, 3 α-L-rhamnosidases, and 1 β-galactosidase, which may be responsible for its ability to convert ginsenosides. In addition, genome annotation revealed other genes of interest, including polysaccharide lyases such as cellulase, GDSL lipase with multifunctional properties such as broad substrate specificity and regiospecificity (Akoh et al., 2004), thiamine biosynthesis protein ThiF (B1) which can synthesize vitamin B1, and nitrite reductase.

General features of Anseongella ginsenosidimutans Gsoil 524T

FeaturesChromosome
Genome size (bp)4,322,684
G + C content (%)49.9
Total genes3,683
Pseudo genes177
Coding sequences (CDSs)3,448
Number of rRNA genes (5S, 16S, 23S)9 (3, 3, 3)
Number of tRNA genes46

Nucleotide sequence accession number

The complete genome sequence of Anseongellaginsenosidimutans Gsoil 524T has been deposited in DDBJ/EMBL/GenBank under the accession number CP042432.

적 요

인삼 토양으로부터 분리한 Anseongellaginsenosidimutans Gsoil 524T 균주의 유전체서열을 분석하였다. 균주 Gsoil 524T의 유전체는 G + C 비율이 49.9%이며, 3,683개의 유전자와 3,448개의 단백질 코딩 유전자, 177개의 위유전자 그리고 58개의 RNA 유전자를 포함한 단일 원형 염색체로 구성되었으며 그 크기는 4,322,684 bp였다. 균주 Gsoil 524T는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자, 고분자 분해 유전자를 가지고 있었다. 이러한 지놈 분석은 메이저 진세노사이드 전환에 관여하는 유전자 특징을 이해하는데 큰 기여가 되었다.

Acknowledgements

This work was supported by grants from the National Institute of Biological Resources, funded by the Ministry of Environment (No. NIBR201801106).

References
  1. Akoh CC, Lee GC, Liaw YC, Huang TH, and Shaw JH. 2004. GDSL family of serine esterases/lipases. Prog. Lipid Res. 43, 534-552.
    Pubmed CrossRef
  2. Anthony R, and Kin FA. 2015. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics. 13, 278-289.
    Pubmed KoreaMed CrossRef
  3. Siddiqi MZ, Cui CH, Park SK, Han NS, Kim SC, and Im WT. 2017. Comparative analysis of the expression level of recombinant ginsenoside-transforming β-glucosidase in GRAS hosts and mass production of the ginsenoside Rh2-Mix. PLoS One. 12, 1371-1385.
    Pubmed KoreaMed CrossRef
  4. Siddiqi MZ, Liu QM, Kang MS, Kim MS, and Im WT. 2016. Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng. Int. J. Syst. Evol. Microbiol. 66, 1125-1130.
    Pubmed CrossRef
  5. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K, and Joubert JJ. 1998. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int. J. Syst. Bacteriol. 48, 165-177.
    Pubmed CrossRef


December 2019, 55 (4)