We report the complete genome sequence of Maritalea myri- onectae HL2708#5, which is a marine microbe from Jeju volcanic rock basal groundwater. The complete genome, consisting of one chromosome and two plasmids, has a size of 3,703,346 bp and G + C content of 52.4%. There were 3,696 protein-coding sequences identified, along with 40 tRNA and six rRNA non-coding genes. The genome contains a β-N- acetylhexosaminase gene (nagZ) for esculin hydrolysis, in addition to two homologs of aromatic l-amino acid decarboxylase for tyrosine and dopamine metabolism, demonstrating its potential as a platform in the production of naturally derived cosmetic components for whitening and anti-inflammation.
Keywords: Maritalea myrionectae, basal groundwater, complete genome, cosmetic component, volcanic rock
Here we report the complete genome of Maritalea myrionectae (strain HL2708#5) isolated from volcanic rock-derived basal groundwater (a coastal aquifer) on Jeju Island, Korea (N 33.5327°, E 126.8204°), which has a bioconversion ability of herbal extract for developing new cosmetic material. In the screening of the marine microorganism, esculin (7-hydroxy- 2-oxo-2H-chromen-6-yl β-d-glucopyranoside; Sigma, E8250) was used as a starting substrate for esculinase test (Koo et al., 2018).
This obligate halophilic strain was analyzed for its 16S rRNA sequence and showed 99% nucleotide similarity to Maritalea myrionectae DSM 19524
Taccording to a previous report (Hwang et al., 2009). We sequenced the genome of M.
myrionectae HL2708#5 according to a method described previously (Yang et al., 2016). The genome was sequenced using the PacBio RS II system (Pacific Biosciences), resulting in a genome coverage of 303-fold. The complete genome consisted of one circular 3,380,026-bp chromosome and two plasmids with 174,698 bp (pHL2708X3) and 148,622 bp (pHL2708Y3), respectively. The whole genome harbors 3,696 protein-coding sequences with an average G + C content of 52.4% (Table 1). Forty tRNA and six rRNA genes were identified on the circular chromosome.
The genome of M. myrionectae HL2708#5 showed 97.2%
similarity to the draft genome of the M. myrionectae type strain DSM 19524
T(GenBank RefSeq assembly accession: GCF_
000423365.1) based on the average nucleotide identity (ANI) values and 99.9% similarity by tetranucleotide analysis (TNA) (https://www.ezbiocloud.net/) (Yoon et al., 2017). MUMmer (Kurtz et al., 2004) was used for counting mutations, demon- strating conserved synteny between the two genomes. Up to 88,984 nucleotide substitutions were detected between the two genomes, and the rate of mutation was one in every 41.6 bp on average in the M. myrionectae HL2708#5 genome (Fig. 1).
Korean Journal of Microbiology (2021) Vol. 57, No. 1, pp. 72-74 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2021.0129 eISSN 2383-9902
Copyright ⓒ 2021, The Microbiological Society of Korea
Complete genome of Maritalea myrionectae strain HL2708#5
Myung Won Lee
1, Dongil Jang
2, and Hyun-Myung Oh
3*
1
Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea
2
Cotde, Inc., Cheonan 31252, Republic of Korea
3
Institute of Liberal Arts Education, Pukyong National University, Busan 48547, Republic of Korea
Maritalea myrionectae HL2708#5 균주의 완성 유전체
이명원
1･ 장동일
2･ 오현명
3*
1
부경대학교 화학과,
2주식회사 콧데,
3부경대학교 기초교양교육원
(Received December 17, 2020; Revised March 16, 2021; Accepted March 16, 2021)
*For correspondence. E-mail: [email protected];
Tel.: +82-51-629-6869
Complete genome of Maritalea myrionectae HL2708#5 ∙
73
Korean Journal of Microbiology, Vol. 57, No. 1 Whereas α-glucosidase (EC3.2.1.20) and β-glucosidase
(EC3.2.1.21) were both positive in the original polyphasic study of M. myrionectae (Hwang et al., 2009), the genomes of M. myrionectae HL2708#5 and M. myrionectae DSM 19524
Tshowed only the presence of α-glucosidase (EC3.2.1.20) in this study. We used the CLgenomics program (www.chunlab.
com) to view the genomic context, and found that β-N- acetylhexosaminidase (nagZ, MXMO3_01499) could be annotated by comparing with the genome of Escherichia coli.
Kyoto Encyclopedia of Genes and Genomes (KEGG) map was
inspected with the CLgenomics program and two protein- coding genes for aromatic l-amino acid decarboxylase (MXMO3_
00495) were found in the Maritalea genomes.
Herbal extracts showed an increase in pH after treatment with M. myrionectae HL2708#5, demonstrating effective bio- conversion (Koo et al., 2018). The rate of melanin biosynthesis (%) was measured and the degree of melanin biosynthesis inhibition was demonstrated for Clerodendrum trichotomum Thunberg, Eriobotrya japonica Lindley, Ilex cornuta Lindley, Lespedeza cuneata G. Don (1832), Phellinus linteus, and
Table 1. Genome features of Maritalea myrionectae strain HL2708#5
Features Circular chromosome Plasmid pHL2708X3 Plasmid pHL2708Y3 Complete genome
Genome size (bp) 3,380,026 174,698 148,622 3,703,346
G + C content (%) 52.7 47.8 51.8 52.4
Total number of genes 3,431 175 136 3,742
Protein-coding genes (CDS) 3,385 175 136 3,696
rRNA genes 6 0 0 6
tRNA genes 40 0 0 40
Fig. 1. Mummer plot of reference genome HL2708#5 (x axis: chromosome, plasmid 1, and plasmid 2) and queried draft genome DSM19524 (y axis).
Nucleotide polymorphisms could be detected 88984 times out of 3,703,346-bp HL2708#5 genomic sequence; nucleotide substitution occurred per 41.6 bp.
74
∙Lee et al.미생물학회지 제57권 제1호
Sambucus williamsii var. coreana (Nakai) Nakai (Koo et al., 2018). Among the herbal extracts tested, Clerodendrum trichotomum Thunberg and Sambucus williamsii var. coreana (Nakai) Nakai showed anti-atopic dermatitis effects shown by thymus-and activation-regulated chemokine (TARC) (R&D Systems, DDN00) and macrophage-derived chemokine (MDC) (R&D Systems, DMD00) in keratinocytes cultures in vitro (Koo et al., 2018).
Using esculinase activity as a hallmark for herbal bioconversion, we identified glycosidic genes as well as tyrosinase/dopamine- related genes in M. myrionectae HL2708#5. In particular, herbal extracts from Clerodendrum trichotomum Thunberg and Sambucus williamsii var. coreana (Nakai) Nakai showed inhibition of melanogenesis and anti-atopic dermatitis effects (Koo et al., 2018). Our genomic and herbal extract studies show the potential of this marine microbe as a bioconversion platform for herbal extracts toward cosmetic applications.
Nucleotide sequence and strain accession numbers The genome sequence of Maritalea myrionectae HL2708#5 (= KCTC 13309BP) was deposited at GenBank under the accession numbers CP021330, CP021331, and CP021332. The strain is available from Cotde, Inc. ([email protected]).
적 요
제주도 용암 해수에서 얻은 미생물인 Maritalea myrionectae HL2708#5의 완전한 염기 서열을 분석하였다. 유전체는 하나 의 원형 염색체와 두 개의 플라스미드로 이루어져 있는데, 전 체 크기는 3,703,346 bp이며 G + C 함량은 52.4%이다. 단백질 을 코딩하는 서열(CDS)은 3,696개이며, 단백질을 코딩하지 않는 40개의 tRNA 및 6개의 rRNA 유전자를 포함하였다. 게 놈은 에스쿨린 가수 분해를 위한 β-N-아세틸 헥소스아미나아 제 유전자(nagZ)와 타이로신(tyrosine)과 도파민(dopamine)
대사를 담당하는 두 개의 방향족 L-아미노산 탈탄산 효소의 상동서열(homolog)을 포함하고 있었다. 이 미생물은 미백이 나 소염 효과가 있는 자연 유래 향장 성분 개발을 위해 쓰일 수 있는 가능성을 보여주었다.
Acknowledgments
Hyun-Myung Oh got supports from “Research Grant of Pukyong National University” (2020).
Conflict of Interest
Hyun-Myoung Oh is Editor in Chief of KJM. He was not involved in the review process of this article. Also, Authors have no conflicts of interest to report.
References
Hwang CY, Cho KD, Yih W, and Cho BC. 2009. Maritalea myrionectae gen. nov., sp. nov., isolated from a culture of the marine ciliate Myrionecta rubra. Int. J. Syst. Evol. Microbiol. 59, 609–614.
Koo CS, Seo S, Kim D, and Jang D. 2018. A novel marine-derived bacterium, and cosmetic compositions using the same. Vol.
KR101918673B1, Republic of Korea.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, and Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5, R12.
Yang JA, Kang I, Moon M, Ryu UC, Kwon KK, Cho JC, and Oh HM.
2016. Complete genome sequence of Celeribacter marinus IMCC12053T, the host strain of marine bacteriophage P12053L.
Mar. Genomics 26, 5–7.
Yoon SH, Ha SM, Lim J, Kwon S, and Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity.
Antonie van Leeuwenhoek 110, 1281–1286.
