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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(2): 208-211

https://doi.org/10.48022/mbl.2306.06001

Received: June 1, 2023; Revised: June 5, 2023; Accepted: June 10, 2023

Complete Genome Sequence of Priestia flexa DMP08 Isolated from Kimchi, Traditional Korean Fermented Vegetables

Junghyun Park1, Jong Hun Kim2, and Do-Won Jeong1*

1Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
2Department of Food Science and Biotechnology, Sungshin University, Seoul 01133, Republic of Korea

Correspondence to :
Do-Won Jeong,       jeongdw@dongduk.ac.kr

Abstract

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Strain Priestia flexa DMP08, isolated from traditional Korean fermented vegetables kimchi, exhibits protease activity and lipase activity. The complete genome of strain DMP08 includes a single circular 3,999,911-bp chromosome without plasmids. The G+C content of the genome is 38.1 mol%. The genome includes 38 protease- and 3 lipase-encoding genes.

Keywords: Priestia flexa, genome, kimchi, protease, lipase

Body

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Priestia flexa was reclassified from Bacillus flexus based on phylogenomic and comparative genomic analyses [1]. P. flexa is endospore-forming and it has been isolated from sources including feces, soil, the upper atmosphere, and sea sediment. The major research interest in P. flexa has concerned enzyme activity, such as of proteases and lipases [2, 3], as well as arsenic remediation [4]. Because of these enzymatic and remediative activities, P. flexa has been suggested to be a useful microorganism for detergents, food technology, pharmaceuticals, and biomedical science [5]. The β-amylase from P. flexa AE-BAF has been used as a food-grade enzyme [3]. However, genomic information on P. flexa is limited. In our previous study, P. flexa strain DMP08 was isolated from kimchi, traditional Korean fermented cabbage [6].

Strain DMP08 exhibited protease activity on tryptic soy agar (Becton Dickinson and Co., USA) supplemented with 2% skim milk (w/v), and lipolytic activity on tributyrin agar (Sigma-Aldrich, USA) supplemented with 1% glyceryl tributyrate (w/v) (Fig. 1). In food fermentation, protease and lipase activities contribute to sensory enhancement through proteolysis and lipolysis [7, 8]. To shed light on its potential as a starter candidate strain for food fermentation, we determined the complete genome sequence of P. flexa DMP08. Whole-genome sequencing was performed using the PacBio Sequel 10K system (PacBio, USA) at CJ Bioscience, Inc. (South Korea). One contig was generated from the obtained sequencing reads (231,996 reads, 352× coverage) by the FLYE assembler (version 2.8.3) in SMRT Link (PacBio) and annotated by using the NCBI Prokaryotic Genome Annotation Pipeline (version 4.6). Annotated gene functions were analyzed using the Clusters of Orthologous Groups (COG) database [9] and Rapid Annotation using Subsystem Technology [10].

Figure 1.Protease (A) and lipase (B) activities of Priestia flexa DMP08. Protease and lipase activity were determined on TSA containing 2% skim milk (w/v) and tributyrin agar containing 1% tributyrin (w/v), respectively. The formation of a clear zone around the colony is determined to be positive enzymatic activity.

The complete genome of P. flexa strain DMP08 consists of a circular 3,999,911-bp chromosome (Table 1). The G+C content of the genome is 38.1 mol%. The average nucleotide identity of the DMP08 genomic sequence showed 99.2% and 74.4% similarity with P. flexa KLBMP 4941 and P. aryabhattai KNUC0118, respectively. The genome was predicted to contain 4,156 open reading frames, 99 tRNA genes, and 37 rRNA genes. COG functionally categorized 3,780 genes and major COG categorizations are related to amino acid transport and metabolism (315 genes, 8.33%), transcription (260 genes, 6.88%), and carbohydrate transport and metabolism (244 genes, 6.46%). The SEED subsystem categorized 1,647 genes and the most abundant subsystem category was related to amino acids and derivatives (308 genes, 18.70%), followed by carbohydrates (254 genes, 15.42%). The genome of P. flexa strain DMP08 contains 38 protease- and 3 lipase-encoding genes (Table 2), and those genes contribute to the protease and lipase activities of P. flexa strain DMP08. P. flexa enzymes, which identified effective enzymes among them, alone or as strains that produce enzymes will help fermented foods or food processing processes.

Table 1 . Genome features of Priestia flexa DMP08.

FeatureValue
Genome size (bp)3,999,911
G+C content (mol%)38.1
Total number of genes4,156
Protein coding genes (CDS)4,015
rRNA genes37
tRNA genes99
Other RNA genes5


Table 2 . Putative protease and lipase genes identified in the genome of Priestia flexa DMP08.

Gene locusE.C. no.ProductCOGGene
Lipase
LZP85_RS002603.1.1.3Triacylglycerol lipaseSlip
LZP85_RS045103.1.1.3Triacylglycerol lipaseSlip
LZP85_RS170253.1.1.5LysophospholipaseIpldB
Protease
LZP85_RS002153.4.-.-Peptidoglycan L-alanyl-D-glutamate endopeptidase CwlKMcwlK
LZP85_RS02900Uncharacterized 42.1-kDa protein in intracellular alkaline protease 3'- regionS
LZP85_RS04965ATP-dependent Clp protease ATP-binding subunit ClpA-like protein CD4AO
LZP85_RS05570Putative membrane protease YugPS
LZP85_RS064853.4.24.89Pro–Pro endopeptidaseSzmp1
LZP85_RS078753.4.-.-Probable peptidoglycan endopeptidase LytES|MlytE
LZP85_RS105953.4.-.-D-gamma-glutamyl-meso-diaminopimelic acid endopeptidase CwlSS|MlytE
LZP85_RS121453.4.21.-Alkaline proteaseOepr
LZP85_RS121703.4.21.107Peptidase DoOdegP
LZP85_RS13055Protease synthase and sporulation protein PAIK
LZP85_RS132353.4.13.19Membrane dipeptidaseEDPEP
LZP85_RS132953.4.24.-Probable inactive metalloprotease YmfFOpqqL
LZP85_RS133353.4.21.92Endopeptidase ClpOclpP
LZP85_RS133753.4.24.-Uncharacterized zinc protease YmxGOpqqL
LZP85_RS134603.4.24.-Probable protease eepMrseP
LZP85_RS13665ATP-dependent protease ATPase subunit HslUO
LZP85_RS136703.4.25.2HslU–HslV peptidaseOhslV
LZP85_RS140503.4.23.-Sporulation sigma-E factor-processing peptidaseSspoIIGA
LZP85_RS14440Protease PrsWS
LZP85_RS149603.4.21.116SpoIVB peptidaseMspoIVB
LZP85_RS152303.4.21.105Rhomboid proteaseS|SgluP
LZP85_RS155953.4.24.78GPR endopeptidaseOgpr
LZP85_RS157453.4.-.-Uncharacterized protease YrrOO
LZP85_RS157503.4.-.-Uncharacterized protease YrrNO
LZP85_RS162253.4.21.53Endopeptidase LaOlon
LZP85_RS162303.4.21.53Endopeptidase LaOlonB
LZP85_RS16235ATP-dependent Clp protease ATP-binding subunit ClpXO
LZP85_RS167353.4.21.-Putative signal peptide peptidase SppAOUsppA
LZP85_RS176953.4.-.-L-Ala–D-Glu endopeptidaseMlytH
LZP85_RS179653.4.21.92Endopeptidase ClpOclpP
LZP85_RS181353.4.21.102C-terminal processing peptidaseMprc
LZP85_RS183703.4.-.-Probable endopeptidase p60M|MlytE
LZP85_RS184903.4.21.-Major intracellular serine proteaseOvpr
LZP85_RS18685Putative zinc metalloprotease YwhCS
LZP85_RS190853.4.21.107Peptidase DoOdegP
LZP85_RS19555Sporulation-specific protease YabGS
LZP85_RS196953.4.24.-ATP-dependent zinc metalloprotease FtsHOftsH
LZP85_RS20345Rhomboid protease GluPS

The Enzyme Commission (EC) number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. The EC numbers are based on the genes of strain DMP08 and gene are assigned by BlastKoALA. The Clusters of Orthologous Group (COG) categorization was generated by annotated gene functions.

Nucleotide Sequence Accession Number. The complete genome sequence of P. flexa DMP08 has been deposited in DDBJ/ENA/GenBank under accession number NZ_CP090431.

Acknowledgments

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This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the High Value-added Food Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (No. 322014-5).

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

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