Staphylococcus xylosus strain DMSX03 was isolated from fermented soybean, meju, and its complete genome sequence was determined. It contains a single circular 2,825,246-bp chromosome and a 48,816-bp plasmid. The G + C content of the genome is 32.76%. Strain DMSX03, having protease and lipase activities, encodes 44 protease and 8 lipase genes. Thus, the genetic background corroborates the enzymatic activities reported for strain DMSX03, making it a potential starter candidate.
Keywords: Staphylococcus xylosus, genome, meju, starter
Coagulase-negative Staphylococcus have been detected predominantly in protein-rich fermented foods (Cocolin et al., 2001; Blaiotta et al., 2004; Corbière Morot-Bizot et al., 2006;
Drosinos et al., 2007). In particular, Staphylococcus xylosus has usually been isolated from fermented sausages, and it displays protease and lipase activities involved in protein and lipid degradation, respectively (Martín et al., 2006; Jeong et al., 2016; dos Santos Cruxen, 2017). These extracellular enzymatic activities contribute to flavor enhancement through the pro- duction of aroma compounds (Sondergaard and Stahnke, 2002;
Jeong et al., 2016). Owing to these properties, S. xylosus has been used in fermented sausage as a meat starter (Leroy et al.,
2017). Here, S. xylosus strain DMSX03 was isolated from fermented soybean, meju, as a starter candidate. Strain DMSX03 exhibited proteolytic and lipolytic activities on tryptic soy agar (BD Diagnostic Systems) containing 1.5% and 4% NaCl, respectively, and its complete genome sequence was determined to confirm its genetic background.
The whole-genome sequencing of S. xylosus strain DMSX03 was performed using the PacBio RSII platform (Pacific Bio- science) at ChunLab, Inc. Two contigs were constructed from 49,384 reads generated using the PacBio system (226.61×
coverage) by HGAP2 assembler in SMRT Link (ver. 7.0.1;
Pacific Bioscience). The NCBI Prokaryotic Genome Annotation Pipeline was used for genome annotation (Tatusova et al., 2016), and Glimmer 3 was used to predict open reading frames (Delcher et al., 1999). Then, a search against the Clusters of Orthologous Groups (COG) database was performed to determine putative protein functions (Tatusov et al., 1997).
The complete genome of strain DMSX03 consists of a single circular 2,825,246-bp chromosome and a 48,816-bp plasmid (Table 1). The G + C content of genome is 32.76%. The genome was predicted to contain 2,704 open reading frames, 59 tRNA genes, and 22 rRNA genes. In total, 2,407 genes were func- tionally assigned to categories on the basis of the COG results.
The genomic fractions in the COG categories related to amino acid transport and metabolism, to carbohydrate transport and
Korean Journal of Microbiology (2021) Vol. 57, No. 1, pp. 52-54 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2021.0120 eISSN 2383-9902
Copyright ⓒ 2021, The Microbiological Society of Korea
Complete genome sequence of Staphylococcus xylosus strain DMSX03 from fermented soybean, meju
Sojeong Heo
1, Jong-Hoon Lee
2, and Do-Won Jeong
1*
1
Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
2
Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
발효콩 메주 유래 Staphylococcus xylosus DMSX03의 유전체 염기서열
허소정
1･ 이종훈
2･ 정도원
1*
1
동덕여자대학교 식품영양학과,
2경기대학교 식품생물공학과
(Received November 23, 2020; Revised December 22, 2020; Accepted December 24, 2020)
*For correspondence. E-mail: [email protected];
Tel.: +82-2-940-4463; Fax: +82-2-940-4610
Genome sequence of Staphylococcus xylosus DMSX03∙
53
Korean Journal of Microbiology, Vol. 57, No. 1 metabolism, and to lipid transport and metabolism were 9.97%
(240 genes), 8.14% (196 genes), and 2.87% (69 genes), respec- tively. Strain DMSX03 possesses 38 protease genes belonging to Enzyme Class (E.C.) 3.4.-.-. and 2 protease genes belonging to E.C. 3.5.1.-. An additional four protease genes were not assigned E.C. numbers. The genome of strain DMSX03 encodes four triacylglycerol lipase (E.C. 3.1.1.3), three lysophospholipase (E.C. 3.1.1.5) and one putative esterase (E.C. 3.1.-.-) genes.
These annotated genes may contribute to the protease and lipase activities of strain DMSX03. Additionally, the DMSX03 genome does not possess α-hemolysin, β-hemolysin, and enterotoxin genes, which have been detected in pathogenic Staphylococcus aureus (Kane et al., 2018). Although hemolysin III family protein gene (DMSX03_RS03685) was detected in DMSX03 genome, it is not clear the contribution of these gene into hemolysis (Robertson et al., 2006). In previous our study, these gene in S. equorum was not related with hemolysis (Jeong et al., 2017). Moreover, DMSX03 did not exhibited the hemolysis, thus we still assumed that hemolysin III family protein gene in DMSX03 may not function in hemolysis. These results suggested that DMSX03 strain might be safe bacteria. The lack of these pathogenicity-related genes is a desired trait of safe candidate starter strains. Consequently, the genome of strain DMSX03 indicates that it utilizes proteins and lipids during fermentation and might contribute to flavor enhancements.
Nucleotide sequence accession number(s)
The complete genome sequence of S. xylosus DMSX03 has been deposited in DDBJ/ENA/GenBank under accession numbers CP060271 and CP060272, and the strain has been deposited in the Korean Culture Center of Microorganisms
under accession number KFCC 11860P.
적 요
Staphylococcus xylosus DMSX03 균주를 메주로부터 분리 하여 유전체를 분석하였다. 균주 DMSX03은 유전체는 약 2.8-Mb 크기의 chromosome과 48-kb 크기의 플라스미드를 보 유하고 있었다. DMSX03 균주의 GC 함량은 32.76%였다. 해 당 균주는 단백질 분해활성과 지방분해활성을 보였고, 유전체 분석 결과 44개의 단백질 분해효소 유전자와 8개 지방분해효 소 유전자를 보유하고 있었다. 이는 DMSX03 균주의 효소활 성에 대한 유전적 배경을 이해하는데 활용될 수 있음을 제공 한다.
Acknowledgments
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education (NRF-2019R1A2C1003639 for DWJ and NRF-2020R1A6A3A13077341 for SH). We thank Lesley Benyon, PhD, from Edanz Group (https://en-author- services.edanzgroup.com/ac) for editing a draft of this manuscript.
References
Blaiotta G, Pennacchia C, Villani F, Ricciardi A, Tofalo R, and Parente E. 2004. Diversity and dynamics of communities of coagulase- negative staphylococci in traditional fermented sausages. J.
Appl. Microbiol. 97, 271–284.
Cocolin L, Manzano M, Cantoni C, and Comi G. 2001. Denaturing gradient gel electrophoresis analysis of the 16S rRNA gene V1 region to monitor dynamic changes in the bacterial population during fermentation of Italian sausages. Appl. Environ. Microbiol.
67, 5113–5121.
Corbière Morot-Bizot S, Leroy S, and Talon R. 2006. Staphylococcal community of a small unit manufacturing traditional dry fermented sausages. Int. J. Food Microbiol. 108, 210–217.
Delcher AL, Harmon D, Kasif S, White O, and Salzberg SL. 1999.
Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27, 4636–4641.
dos Santos Cruxen CE, Funck GD, da Silva Dannenberg G, Haubert L, de Lima Marques J, Kroning IS, Chaves FC, da Silva WP, and Fiorentini, AM. 2017. Characterization of Staphylococcus xylosus Table 1. Genome features of Staphylococcus xylosus strain DMSX03
Feature Value
Genome size (bp) 2,874,062
G + C content (%) 32.76
Number of plasmids 1
Open reading frames 2,704
CDS assigned by COG 2,407
rRNA genes 22
tRNA genes 59
Abbreviations: CDS, coding DNA sequence; COG, Cluster of Orthologous Groups of proteins.
54
∙Heo et al.미생물학회지 제57권 제1호
LQ3 and its application indried cured sausa. LWT 86, 538–543.
Drosinos EH, Paramithiotis S, Kolovos G, Tsikouras I, and Metaxopoulos I. 2007. Phenotypic and technological diversity of lactic acid bacteria and staphylococci isolated from traditionally fermented sausages in southern Greece. Food Microbiol. 24, 260–270.
Jeong DW, Heo S, Ryu S, Blom J, and Lee JH. 2017. Genomic insights into the virulence and salt tolerance of Staphylococcus equorum.
Sci. Rep. 7, 5383.
Jeong DW, Lee B, Her JY, Lee KG, and Lee JH. 2016. Safety and technological characterization of coagulase-negative staphylococci isolates from traditional Korean fermented soybean foods for starter development. Int. J. Food Microbiol. 236, 9–16.
Kane TL, Carothers KE, and Lee SW. 2018. Virulence factor targeting of the bacterial pathogen Staphylococcus aureus for vaccine and therapeutics. Curr. Drug Targets 19, 111–127.
Leroy S, Vermassen A, Ras G, and Talon R. 2017. Insight into the genome of Staphylococcus xylosus, a ubiquitous species well adapted to meat products. Microorganisms 5, 52.
Martín B, Garriga M, Hugas M, Bover-Cid S, Veciana-Nogués MT,
and Aymerich T. 2006. Molecular, technological and safety characterization of Gram-positive catalase-positive cocci from slightly fermented sausages. Int. J. Food Microbiol. 107, 148–
158.
Robertson KP, Smith CJ, Gough AM, and Rocha ER. 2006. Charac- terization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. Infect. Immun. 74, 2304–2316.
Søndergaard AK and Stahnke LH. 2002. Growth and aroma production by Staphylococcus xylosus, S. carnosus and S. equorum-a comparative study in model systems. Int. J. Food Microbiol. 75, 99–109.
Tatusov RL, Koonin EV, and Lipman DJ. 1997. A genomic perspective on protein families. Science 278, 631–637.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624.
