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Complete genome sequence of Niabella ginsenosidivorans BS26T, a ginsenoside-converting bacterium, isolated from compost
Korean J. Microbiol 2018;54(4):465-467
Published online December 31, 2018
© 2018 The Microbiological Society of Korea.

Young-Woo Lee1, Muhammad Zubair Siddiqi1,2, Qing-Mei Liu1,2, Dae-Cheol Kim1, and Wan-Taek Im1,2,*

1Department of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea,
2AceEMzyme Co., Ltd., Academic Industry Cooperation, Anseong 17579, Republic of Korea
Correspondence to: E-mail: wandra@hknu.ac.kr; Tel.: +82-31-670-5335; Fax: +82-31-670-5339
Received November 20, 2018; Revised November 30, 2018; Accepted December 6, 2018.
Abstract

An orange-colored, rod-shaped strain, designated Niabella ginsenosidivorans BS26T, was isolated from compost. Strain BS26T showed the ability to convert major ginsenosides to minor ginsenosides, and its whole genome was sequenced. The whole genome of N. ginsenosidivorans BS26T consists of a single circular chromosome of 5,627,734 bp with 44.48% G + C content. Based on the complete genome sequence of strain BS26T, we found several glycosides hydrolase-encoding genes that might involve in the conversion of major ginsenosides into minor ginsenoside and deliberate its strong pharmacological effects.

Keywords : Niabella ginsenosidivorans, complete genome, compost, glycoside hydrolase, PacBio RS II
Body
he genus Niabella was first described by Kim et al. (2007). Species of this genus are non-flagellated, non-spore-forming, and Gram negative. The DNA G + C content ranges between 42.0 mol% and 47.5 mol%. Currently, the genus comprises of 10 recognized species with published names (LPSN, http://www.bacterio.net/niabella.html), which were commonly isolated from various sources such as soil, medicinal leeches, and lake water (Kim et al., 2007; Siddiqi and Im, 2016).

To identify a ginsenoside transforming positive bacterium, a Gram-negative bacterium, N. ginsenosidivorans BS26T, was isolated from compost (decayed feedstuff) in the Republic of Korea. N. ginsenosidivorans BS26T was orange coloured, non-spore forming and non-motile rod bacterium. Based on the production of minor ginsenosides from major ginsenosides (Yi et al., 2015; Siddiqi et al., 2017), strain N. ginsenosidivorans BS26T was selected for a whole genome study to identify the target functional genes. Whole genome sequence analysis showed more than 40 glycoside hydrolases that may involve in the conversion of ginsenosides. This strain is available from the host institute and from two culture collections (= KACC 16620T = JCM 18199T).

The genomic DNA of N. ginsenosidivorans BS26T was extracted and purified with the genomic DNA extraction kit (Biofact), and was sequenced using the Pacific Biosciences RSII platform. And a library was constructed according to the Pacific Biosciences RSII Sequencing method manual. The general features about the complete genome sequencing and library construction are available at the JGI website (https://www.jgi.doe.gov). PacBio SMRT Analysis (version 2.3.0) was used with default options for sequence reads assembly, and the protein coding sequences (CDSs) were predicted by Glimmer 3.02 (Delcher et al., 1999). The genome sequence was annotated through the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAP; http://www.ncbi.nlm.nih.gov/books/NBK174280/). The tRNAs and rRNAs were predicted by using rRNAmmer and tRNAscan-SE, respectively.

The complete genome of N. ginsenosidivorans BS26T consists of one circular chromosome of 5,627,734 bp with 44.48% G + C content. Out of the 4,756 predicted genes, 4,704 were protein-coding genes (CDS), and 49 were RNAs. Moreover, 85 pseudogenes were also identified (Fig. 1). The majority of the protein-coding genes (98.81%) were assigned with a putative function, while the remaining predicted genes were annotated as hypothetical or conserved hypothetical proteins. The genome statistics are presented in Table 1. Analysis of the complete genome sequence showed many glycoside hydrolase-encoding genes including 14 β- glucosidases, 11 α-glucosidases, 8 β- xylosidases, 8 α-arabinofuranosidases, and 1 β-arabinofuranosidase, which may be responsible for its ability to convert ginsenosides. In addition, the genome also encoded a nitrite reductase (NADH) small subunit, mercury resistance protein (MerC), quinone reductase or related Zn-dependent oxidoreductase, putative oxidoreductase, ferredoxin-NADP reductase, sulfatase, sulfite reductase, sulfate degradation, Clp endopeptidase (endonuclease/exonuclease), thiol-disulfide oxidoreductase, protein involved in L-lysine biosynthesis, and multiple antibiotic resistance proteins. The presence of these genes shows the importance of the bacterial group represented by this strain for the cycling of organic and inorganic elements.

General features of Niabella ginsenosidivorans BS26T

 FeaturesChromosome
Genome size (bp)5,627,734
DNA coding region (bp)4,908,857
G + C content (%)44.48
Total genes4,756
Pseudo genes85
Coding sequences (CDSs)4,704
Number of rRNA genes (5S, 16S, 23S)6 (2, 2, 2)
Number of tRNA genes43

Fig. 1.

Graphical map of the chromosome of Niabella ginsenosidivorans BS26 T. The rings from the outside to the center show the following: genes on the forward strand (colored by COG category), genes on the reverse strand (colored by COG category), RNA genes (tRNAs, green; rRNAs, red; other RNAs, black), GC content, and GC skew.


The availability of the whole genome sequence of N. ginsenosidivorans BS26T will allow further functional and comparative analyses to understand the genomic traits well involved in the conversion of plant secondary metabolites as described by Siddiqi et al. (2017).

Nucleotide sequence accession number

The complete genome sequence of Niabella ginsenosidivorans BS26T has been deposited at DDBJ/EMBL/NCBI GenBank under accession number CP015772.

적 요

퇴비로부터 분리한 Niabella ginsenosidivorans BS26T 균주의 유전체서열을 분석하였다. 균주 BS26T의 유전체는 G + C 비율이 44.48%이며, 4,800개의 유전자와 4,704개의 단백질 코딩 유전자, 85개의 위유전자 그리고49개의 RNA유전자를 포함한 단일 원형 염색체로 구성되었으면 그 크기는 5,627,734 bp였다. 균주 BS26T는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자를 가지고 있었다. 이러한 유전체 분석은 주요 진세노사이드 전환에 관여하는 유전자 특징을 이해하는데 큰 기여가 되었다.

Acknowledgements

This research was supported by the project for the survey and excavation of Korean indigenous species of the National Institute of Biological Resources (NIBR) and the Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ012283) of the Rural Development Administration, Republic of Korea.

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