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Complete genome sequence of Tetragenococcus halophilus CY54 showing protease and aminopeptidase activity
Korean J. Microbiol. 2021;57(3):223-225
Published online September 30, 2021
© 2021 The Microbiological Society of Korea.

Do-Won Jeong1, Sojeong Heo1, Tae Jin Kim2, and Jeong Hwan Kim2,3*

1Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
2Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
3Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
Correspondence to: E-mail: jeonghkm@gnu.ac.kr; Tel.: +82-55-772-1904; Fax: +82-55-772-1909
Received August 5, 2021; Revised August 25, 2021; Accepted August 27, 2021.
Abstract
Tetragenococcus halophilus CY54 isolated from Korean traditional fermented seafood, meoylchi-jeotgal, exhibited protease and aminopeptidase activity. The complete genome of strain CY54 contains a single circular 2,620,793-bp chromosome without plasmids. The G + C content of the genome is 36.0% and encodes 21 protease and 14 aminopeptidase genes.
Keywords : Tetragenococcus halophilus, aminopeptidase, genome, meoylchi-jeotgal, protease
Body

Tetragenococcus halophilus is a halophilic lactic acid bacteria and has been widely detected in high-salt fermented food such as soy sauce in Japan, doenjang in Korea, fish sauce in Southeast Asia (Sugiiyama, 1984; Jeong et al., 2017a; Rodpai et al., 2021). Tetragenococcus halophilus as a starter culture contributed to the sensory properties in fermented foods via aroma compounds productions (Udomsil et al., 2011; Jeong et al., 2017b, 2019). It was well known that extracellular protease activities contribute to sensory enhancement through proteolysis for taste and aroma compounds (Yuceer et al., 2009). The extracellular protease activities exhibited strain-specificity in previous studies (Jeong et al., 2014, 2017b).

Therefore, in current study, T. halophilus CY54, exhibiting strong protease activity, was isolated from Korean traditional fermented seafood, myeolchi-jeotgal purchased at a local market in Jinju, Korea, and studied to secure a starter candidate. Additionally, strain CY54 showed the aminopeptidase activity, which produced the active compounds during fermentation while reduced the bitterness. To understand the genetic background on strain-specific protease activity, we determined the genome sequence of strain CY54. The whole-genome sequencing of T. halophilus strain CY54 was performed using the PacBio Sequel 10K system (PacBio) at ChunLab, Inc. One contig was generated from generated PacBio sequencing reads (89,268 reads and 292× coverage) by the Flye assembler (version 2.8.3) in SMRT Link (PacBio) and annotated by NCBI Prokaryotic Genome Annotation Pipeline (version 4.6) (Tatusova et al., 2016). Annotated gene functions were analyzed by the Clusters of Orthologous Groups (COG) database (Tatusov et al., 1997) and the Rapid Annotation using Subsystem Technology (Aziz et al., 2008).

The complete genome of T. halophilus CY54 consists of a single circular 2,620,793-bp chromosome with a G + C content of 36.0% (Table 1). The genome was predicted to contain 2,823 open reading frames, 62 tRNA genes, and 15 rRNA genes. Total 2,776 genes were categorized functionally by COG and the major groups are related to carbohydrate transport and metabolism (362 genes, 13.0%), as well as replication, recombination, and repair (285 genes, 10.3%), and amino acid transport, and metabolism (198 genes, 7.13%). The SEED subsystem categorized 1,127 genes and the most abundant subsystem category is related to carbohydrates (219 genes, 19.4%). The next abundant subsystem category is related to protein metabolism (166 genes, 14.7%).

Genome features of Tetragenococcus halophilus CY54

Feature Value
Genome size (bp) 2,620,793
G + C content (%) 36.0
Number of plasmids 0
Open reading frames 2,823
CDSs assigned by COG 2680
CDSs assigned by SEED 1127
rRNA genes 15
tRNA genes 62

Abbreviations: CDS, coding DNA sequence; COG, Cluster of Orthologous Groups of proteins.



Tetragenococcus halophilus CY54 genome possesses 21 protease genes and 14 aminopeptidase genes (Table 2). One protease, CAAX protease (KV134_07470), gene and two aminopeptidases, tripeptide aminopeptidase (KV134_05570) and Succinyl-diaminopimelate desuccinylase (KV134_00680), genes were identified in strain CY54. In contrast, those genes were not detected in the published genome of strain NBRC 12172 (GenBank Accession No. NC_016052.1). Thus, we assumed that strain-specific 35 protease genes conferred more robust protease and aminopeptidase activity of strain CY54.

Putative protease and aminopeptidase genes identified in two Tetragenococcus halophilus genomes

Gene product EC No. Gene locus Homology (%)
CY54 NBRC 12172
Protease
Serine protease HtrA 2.7.1.6 KV134_00715 TEH_RS01225 99.8
Protease 3.4.-.- KV134_12940 TEH_RS00355 98.5
Protease 3.4.-.- KV134_12935 TEH_RS00350 100
Putative dipeptidase YtjP 3.4.13.- KV134_10030 TEH_RS01190 100
Membrane dipeptidase 3.4.13.19 KV134_03650 TEH_RS09475 97.5
Serine protease 3.4.21.- KV134_05650 TEH_RS07180 98.2
Tripeptidase 3.4.21.102 KV134_05165 TEH_RS07695 98.1
Peptidase Do 3.4.21.107 KV134_00715 TEH_RS01225 99.8
Prepilin peptidase 3.4.23.43, 2.1.1.- KV134_12320 TEH_RS12395 100
Metalloprotease 3.4.24.- KV134_03575 TEH_RS09550 99.8
Metalloprotease 3.4.24.- KV134_12005 TEH_RS12095 99.1
Metalloprotease 3.4.24.- KV134_12740 TEH_RS00165 99.8
Putative zinc metalloproteinase in scaA 5'region 3.4.24.- KV134_10490 TEH_RS10490 100
Insulysin 3.4.24.56 KV134_12745 TEH_RS00170 100
CAAX protease 3.4.24.84 KV134_07470 - -
Threonine endopeptidase 3.4.25.2 KV134_05230 TEH_RS07625 100
ATP-dependent protease KV134_12355 TEH_RS04620 99.5
Metallopeptidase KV134_09850 TEH_RS03125 100
Ribosomal-processing cysteine protease Prp KV134_09465 TEH_RS03510 100
Serine protease KV134_11685 TEH_RS11745 98.2
YhfC family intramembrane metalloprotease KV134_04415 TEH_RS08370 96.6
Aminopeptidase
Aminopeptidase PepS 3.4.11.- KV134_09245 TEH_RS03715 97.3
Tripeptide aminopeptidase 3.4.11.4 KV134_05570 -
Prolyl aminopeptidase 3.4.11.5 KV134_12300 TEH_RS12375 100
Glutamyl aminopeptidase 3.4.11.7 KV134_00695 TEH_RS01205 100
Aminopeptidase P family protein 3.4.11.9 KV134_09400 TEH_RS03570 100
Methionine aminopeptidase 3.4.11.18 KV134_09230 TEH_RS03730 99.6
Xaa-Pro dipeptidase 3.4.13.9 KV134_04430 TEH_RS08355 97
Isoaspartyl dipeptidase 3.4.19.- KV134_01205 TEH_RS01745 99.7
Pyroglutamyl-peptidase I 3.4.19.3 KV134_02440 TEH_RS02435 100
Pyroglutamyl-peptidase I 3.4.19.3 KV134_02450 TEH_RS02445 89.7
Aminopeptidase 3.4.22.40 KV134_08310 TEH_RS04590 100
Aminopeptidase 3.4.22.40 KV134_12485 TEH_RS12570 97.7
Group B oligopeptidase PepB 3.4.24.- KV134_09695 TEH_RS03270 98.2
Succinyl-diaminopimelate desuccinylase 3.5.1.18 KV134_00680 -

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 CY54. Homology means the amino acid sequence homology between two strains.

Abbreviation: –, not identified or determined.



Nucleotide sequence accession numbers

The complete genome sequence of T. halophilus CY54 has been deposited in DDBJ/ENA/GenBank under accession number CP078164, and the strain has been deposited in the Korean Culture Center of Microorganisms under accession number KCCM 90481.

적 요

한국의 멸치 젓갈에서 protease와 aminopeptidase 활성을 보이는 Tetragenococcus halophilus CY54 균주를 분리하고 유전체의 염기 서열을 해독하였다. Tetragenococcus halophilus CY54 유전체는 2,620,793 bp 크기이며, 플라스미드를 보유하지 않았다. CY54 균주의 GC 함량은 36.0%이고, 21개의 단백질 분해 유전자와 14개의 aminopeptidase 유전자가 있는 것으로 추정되었다.

Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. NRF-2020R1A2C100826712). Kim TJ was supported by full time graduate student scholarship from Gyeongsang National University.

Conflict of Interest

The authors have no conflict of interest to report.

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