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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(4): 505-508

https://doi.org/10.48022/mbl.2408.08011

Received: August 13, 2024; Revised: September 30, 2024; Accepted: October 3, 2024

Complete Genome Sequence of Leuconostoc mesenteroides MSL129 Isolated from Kimchi

Se-Young Kwun1,3, Eun-Hee Park2,3, and Myoung-Dong Kim2,4*

1Department of Food Biotechnology and Environmental Science, Kangwon National University, Chuncheon 24341, Republic of Korea
2Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
3Research and Development Institute, Metascreen Inc., Chuncheon 24341, Republic of Korea
4Institute of Fermentation and Brewing, Kangwon National University, Chuncheon 24341, Republic of Korea

Correspondence to :
Myoung-Dong Kim,       mdkim@kangwon.ac.kr

Abstract

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The Leuconostoc mesenteroides MSL129, isolated from kimchi, has the potent activity of converting daidzin to daidzein. A complete genome sequence of L. mesenteroides MSL129 has a circular chromosome (2,010,741 bp) and two plasmids. Comparative genomic analysis suggested similarities and unique regions compared to other Leuconostoc species. The carbohydrate-active enzyme gene analysis revealed that the L. mesenteroides MSL129 genome has 33 glycoside hydrolase genes harboring β-glucosidase encoding genes. This genomic information was deposited at NCBI GenBank (CP128560-CP128562). These results contribute to the understanding of the genomic characteristics of L. mesenteroides in the food and biotechnology industries.

Keywords: Leuconostoc mesenteroides, complete genome sequence, lactic acid bacteria, β-glucosidase, daidzein

Body

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Leuconostoc mesenteroides, a Gram-positive, facultatively anaerobic, heterofermentative lactic acid bacterium, has been the subject of extensive research due to its metabolic capabilities and versatile applications in the food and biotechnology industries [1, 2]. Comparative genomic studies have revealed the genetic basis for the unique metabolic capabilities of Leuconostoc species, particularly their ability to ferment a variety of carbohydrates efficiently and produce valuable metabolites such as dextran and lactic acid [3]. In the previous report, the L. mesenteroides MSL129 (KCTC13578BP), isolated from kimchi, showed potent β-glucosidase activity to convert daidzin to daidzein [4].

Whole genome sequencing of L. mesenteroides MSL129 was performed using the PacBio Sequel II platform (Pacific Biosciences, USA), and the de novo genome assembly was performed using FALCON (v.2.1.4). The open reading frame was annotated using Prokka (v1.14.6) [5]. The chromosome was compared and visualized using BLAST Ring Image Generator (BRIG, v.0.95) [6]. The average nucleotide identity (ANI) values among the L. mesenteroides MSL129 and related species were calculated by the Orthologous Average Nucleotide Identity Tool (OAT, v.0.93.1) [7]. The genomic data of L. mesenteroides and other Leuconostoc species were obtained from the National Center for Biotechnology Information (NCBI, USA). This genomic information was deposited at NCBI GenBank (BioProject: PRJNA947117 and Biosample: SRR12817438).

The genome of L. mesenteroides MSL129 consists of one chromosome of 2,010,741 bp and two plasmids of 50,285 and 17,970 bp. Genome coverage was 446.28 fold, and the GC contents of the chromosome and the two plasmids were 37.8, 35.3, and 33.0%, respectively. The genome was predicted to contain 1,977 open reading frames, 71 tRNA, and 12 rRNA genes. Two plasmids contained 61 and 21 genes, probably encoding proteins, respectively.

Table 1 . Genome features of L. mesenteroides strains.

StrainTotal length (Mb)ChromosomePlasmidGenBank Accession No.
Length (Mb)G+C Content (%)Protein coding genesrRNA genestRNA genes
MSL1292,082,0137.71,97712712CP128560
KNU-22,101,9737.91,95712714CP089782
SRCM1027332.061.9937.81,98112702CP028251
ATCC82932.082.0437.71,98612701CP000414
DRC15061.981.8937.71,83812703CP014611
DSM204841.851.8238.01,72412701CP012009

Fig. 1 shows the ANI value and multiple alignments of the L. mesenteroides MSL129 genome with nine other Leuconostoc genomes. The result suggests that the L. mesenteroides MSL129 genome is like the genomes of other L. mesenteroides. Fig. 2 shows a circular comparison map of the L. mesenteroides MSL129 genome and other Leuconostoc genomes. Several regions found in L. mesenteroides MSL129 do not occur within the other Leuconostoc genomes. Most of these regions were associated with hypothetical proteins. Among these, the nucleotide sequences at 607,502 bp, 612,498 bp, and 613,705 bp were annotated as UDP-Gal: α-D-GlcNAc-diphosphoundecaprenol β-1,3-galactosyltransferase (EC 2.4.1.303), putative glycosyltransferase EpsF, and serine O-acetyltransferase (EC 2.3.1.30), respectively (Fig. 2).

Figure 1.Orthologous average nucleotide identity (OrthoANI) heat map between L. mesenteroides MSL129 and other closely related species. ‘Closely related species’ were defined as strains with an ANI value of 74% or more significant compared to L. mesenteroides MSL129. The genome of L. mesenteroides MSL129 was analyzed and compared with five other L. mesenteroides strains and four Leuconostoc strains. Leuconostoc strains whose complete genome sequences were registered in NCBI were used for comparison.
Figure 2.Genome comparisons between L. mesenteroides MSL129 and other Leuconostoc strains visualized using BRIG. The marked region (*) was found only in the L. mesenteroides MSL129 genome.

To search for genes encoding carbohydrate-active enzymes (CAZyme), the dbCAN3 annotation tool [8] was used. In L. mesenteroides strains, five CAZyme families of encoding genes were found (Fig. 3A): Glycoside hydrolases (GH), Glycosyltransferases (GT), Carbohydrate esterases (CE), Auxiliary activities (AA) and Carbohydrate-binding modules (CBM). The L. mesenteroides MSL129 genome contained 57 CAZyme genes: 33 of GH, 21 of GT, 1 of CE, and 2 of CBM. GH was known as catabolic enzymes that catalyze the cleavage of glycosidic bonds [9]. L. mesenteroides MSL129 shows higher numbers of GH1, GH13_31, GH25, and GH65 genes than other L. mesenteroides strains (Fig. 3B). It was also revealed that L. mesenteroides MSL129 has the gene for β-glucosidase (GH3), which can convert daidzin to daidzein.

Figure 3.(A) Number of carbohydrate-active enzyme (CAZyme) genes in L. mesenteroides MSL129 and other strains (GH, glycoside hydrolase; GT, glycosyltransferase; CE, carbohydrate esterase; CBM, carbohydrates-binding module AA, auxiliary activities). (B) Heatmap for glycoside hydrolases (GH) gene distribution in L. mesenteroides MSL129 and other strains.

In conclusion, genome-scale data obtained in this study will facilitate a deeper understanding of the genetic basis for the valuable properties of L. mesenteroides MSL 129, which is essential for developing innovative applications in the food and biotechnology industries.

Nucleotide Sequence Accession Number

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The complete genome sequence of L. mesenteroides MSL129 has been deposited in DDBJ/ENA/GenBank under accession number CP128560 (chromosome), CP128561 (plasmid), and CP128562 (plasmid).

Acknowledgments

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This research was financially supported by the Ministry of SMEs and Startups (MSS), Korea, under the “Regional Specialized Industry Development Program (R&D, R0005969)” supervised by the Korea Institute for Advancement of Technology (KIAT).

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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