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Draft genome sequence of isomaltooligosaccharides-synthesizing Weissella cibaria YRK005
Korean J. Microbiol. 2022;58(1):55-57
Published online March 31, 2022
© 2022 The Microbiological Society of Korea.

Yoonjeong Cho and Young-Seo Park*

Department of Food Science and Biotechnology, Gachon University, Seongnam 13120, Republic of Korea
Correspondence to: E-mail: ypark@gachon.ac.kr; Tel.: +82-31-750-5378; Fax: +82-31-750-5389
Received January 7, 2022; Revised March 15, 2022; Accepted March 23, 2022.
Abstract
Weissella cibaria YRK005 is a bacterium isolated from young radish kimchi; it produces isomaltooligosaccharides when sucrose and maltose are present in the growth medium. In this study, the genome of W. cibaria YRK005 was sequenced using the Illumina MiSeq platform. The genome assembly revealed 31 contigs. The genome was found to be 2,358,664 bp in size with a G + C content of 45.0% and 2,148 protein-coding sequences, 77 tRNA genes, and 13 rRNA genes. Weissella cibaria YRK005 was also found to harbor genes encoding glucansucrase, an enzyme that catalyzes the synthesis of isomaltooligosaccharides.
Keywords : Weissella cibaria, genome sequence, glucansucrase, isomaltooligosaccharides, lactic acid bacteria
Body

The bacterial genus Weissella was first proposed in 1993. This genus belongs to the phylum Firmicutes, class Bacilli, order Lactobacillales, and family Leuconostocaceae. Currently, the genus Weissella comprises 24 species of heterofermentative Leuconostoc-like lactic acid bacteria (Teixeira et al., 2021). Weissella cibaria is a Gram-positive, catalase-negative, non-motile, and short rod-shaped bacteria (Björkroth et al., 2002). Some Weissella strains can synthesize dextran or non-digestible oligosaccharides in reactions catalyzed by glycosyltransferases [EC 2.4] like glucansucrase and fructansucrase (Zarour et al., 2017). Weissella cibaria YRK005 has been previously isolated from young radish kimchi; in the presence of sucrose and maltose, the bacteria synthesize isomaltooligosaccharides that are made up of α-1,4 and α-1,6 linkages (Park and Park, 2021). Therefore, W. cibaria YRK005 was predicted to possess glycosyltransferase activity.

In the present study, genomic DNA was isolated from W. cibaria YRK005 using the AccuPrep Genomic DNA Extraction kit (Bioneer). Whole-genome sequencing was conducted by Sanigen Co., Ltd. using the Illumina MiSeq platform. Quality control of the raw data was performed using FastQC v0.11.8 (https://github.com/s-andrews/FastQC). The filtered reads were trimmed using Trimmomatic v0.38 (Bolger et al., 2014). De novo genome assembly was accomplished using Spades v3.13.0. Quality check of the genome assembly to check for contamination was performed using Burrows-Wheeler Aligner v0.7.17 and Samtools v1.9 (Li et al., 2009). The NCBI Prokaryotic Genome Annotation Pipeline v4.12 was used for annotation using the best-placed reference protein set (GeneMarkS-2+). Average nucleotide identity was analyzed using OrthoANI v0.93.1 (Lee et al., 2016) with the database of NCBI reference genomes (RefSeq) of Weissella sp. (https://www.ncbi.nlm.nih.gov/datasets/genomes/). EggNOG-mapper v2.1.6 based on the eggNOG v5.0 database (Huerta-Cepas et al., 2019) was used to classify the protein-coding sequences into clusters of orthologous groups (COG) categories depending on their functional characteristics. The dbCAN2 meta server was used for carbohydrate-active enzyme (CAZyme) annotation (Zhang et al., 2018).

The analysis of the genome sequence of W. cibaria YRK005 revealed that the genome was composed of 31 contigs with a total length of 2,358,664 bp. Genome coverage was 333.7×, and the overall G + C content was 45.0%. Briefly, 2,148 protein-coding sequences were detected in the genome that included 13 rRNAs (seven 5S rRNAs, one 16S rRNA, and five 23S rRNAs) and 77 tRNAs (Table 1). OrthoANI revealed the highest identity (99.92%) of W. cibaria YRK005 with W. cibaria CMS3. Among the 1,816 genes assigned to COG categories, 281 genes were involved in cellular processes and signaling, 689 in metabolism, and 407 in information storage and processing. The remaining 439 genes were poorly characterized because their functions were unclear, or they did not belong to COG annotations. CAZyme annotation was performed using three tools, namely HMMER, DIAMOND, and Hotpep, that identified 47 enzymes common to the three databases that were considered CAZymes. Only one enzyme was classified in glycoside hydrolase family 70, which synthesize α-glucan. The enzyme was encoded by a gene consisting of 4,347 bp and was annotated as “KxYKxGKxW signal peptide domain-containing protein.”

General genomic features of W. cibaria YRK005

Features Chromosome
Genome size (bp) 2,358,664
Contigs 31
G + C content (%) 45.0
rRNA genes (5S, 16S, 23S) 13 (7, 1, 5)
tRNA genes 77
Protein-coding sequences 2,148
Genes assigned to COGs 1,816


The annotation results revealed that the KxYKxGKxW-type peptide was associated with glucansucrase. This type of motif was reported in the signal peptide present in the N-terminal region of some glucansucrases (Bechtner, 2021). Thus, W. cibaria YRK005 harbors the glucansucrase gene, and the isomaltooligosaccharides produced by this strain can potentially be used as prebiotics because of their non-digestible property. Weissella cibaria YRK005 was deposited in the Korean Culture Center of Microorganisms under the deposit number KCCM 43404.

Nucleotide sequence accession number

The genome sequence of W. cibaria YRK005 was deposited in NCBI GenBank under the accession number JACGMM 010000001-JACGMM010000031.

적 요

열무 김치에서 분리한 Weissella cibaria YRK005는 배지에 sucrose와 maltose를 첨가하였을 때, 이소말토올리고당을 생산하였다. Weissella cibaria YRK005의 유전체는 총 31개의 contig로 구성되어 있고 총 길이는 2,358,664 bp였다. 유전체의 G + C 비율은 45.0%로 나타났으며, 단백질 코딩 유전자 2,148개와 77개의 tRNA 유전자, 13개의 rRNA가 확인되었다. Weissella cibaria YRK005는 이소말토올리고당을 생산할 수 있는 glucansucrase 유전자를 가지는 것으로 확인되었다.

Acknowledgments

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2019R1A2C1004950).

Conflict of Interest

The authors have no conflict of interest to report.

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March 2022, 58 (1)