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Complete genome sequence of a novel polysaccharide-degrading marine bacterium, Echinicola strongylocentroti MEBiC08714
Korean J. Microbiol. 2019;55(4):448-450
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Seung Seob Bae1, Yoon-hee Jung1, Jung-Hee Woo2, and Kyunghwa Baek1*

1National Marine Biodiversity Institute of Korea, Chungcheongnamdo 33662, Republic of Korea
2Marine Industry Research Institute for East Sea Rim (MIRE) 22, Gyeongbuk 36315, Republic of Korea
Correspondence to: *E-mail: kyunghwabaek@mabik.re.kr;
Tel.: +82-41-950-0748; Fax: +82-41-950-0747
§Supplemental material for this article may be found at http://www.kjom.org.
Received November 27, 2019; Revised December 6, 2019; Accepted December 6, 2019.
Abstract

Echinicola strongylocentroti MEBiC08714T isolated from sea urchin Strongylocentrotus intermedius can degrade polysaccharides like agar, alginate, and starch. The genome was sequenced to identify the genomic basis of this activity. The genome is composed of 6,252,144 bp, 4,695 protein-coding sequences, and 44.1 mol% G + C content. The strain MEBiC08714T encodes a large set of carbohydrate active enzymes including 187 glycosyl hydroxylases and 22 polysaccharide lyases. The large diversity of hydrolytic enzymes supports the use of E. strongylocentroti MEBiC08714T as a candidate for biotechnological applications in enzymatic polysaccharide conversion.

Keywords : Echinicola, complete genome, degradation, polysaccharide
Body

The genomic data retrieved from members of the phylum Bacteroidetes revealed that they are commonly primary polysaccharide degraders due to the prediction of a large number and diversity of carbohydrate-degrading enzymes in their genomes (Fernández-Gómez et al., 2013; Lapébie et al., 2019). The genus Echinicola is a member of the Bacteroidetes phylum, which currently contains five species with validly published names (www.bacterio.net/echinicola). To date, five genomes of Echinicola species have been released in the NCBI gene database. Echinicola strongylocentroti MEBiC08714T was isolated from a sea urchin Strongylocentrotus intermedius collected at the west edge of the East Sea of Korea (Jung et al., 2017). Strain MEBiC08714T can degrade polysaccharides like agar, alginate, and starch. To provide a genomic basis for microbial polysaccharide degradation, we report the complete genomic sequence of the Bacteroidetes member Echinicola strongylocentroti MEBiC08714T.

Genomic DNA was isolated from cells grown on marine agar at 25°C for two days using a Wizard Genomic DNA purification kit (Promega). The 20-kb sequencing library was constructed using a PacBio DNA Template Prep Kit 1.0. The library was sequenced using 8-well-SMART Cell v3 in PacBio RSII. Sequencing data were assembled using PacBio SMRT Analysis 2.3.0 with the HGAP3 protocol. Library construction and sequencing were performed by Macrogen, Inc. Sequencing depth was 118.0X. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and deposited into NCBI GenBank (accession number CP030041). The genome of strain MEBiC08714T consists of a single circular chromosome composed of 6,252,144 bp, 4,695 coding sequences, 12 rRNAs, 45 tRNAs and three noncoding RNA with 44.1 mol% G + C content (Table 1).

General genomic features of Echinicola strongylocentroti MEBiC08714T

AttributeValue
Genome assembly
Assemble methodSMRT analysis v. 2.3.0 (HGAP3)
Genome coverage118.0X
Genome features
Genome seize (bp)6,252,144
G + C content (mol%)44.1
No. of contigs1
No. of coding sequence (CDS)4,695
No. of tRNA genes45
No. of rRNA (5S, 16S, 23S) genes12 (4, 4, 4)
No of ncRNA genes3
Pseudogenes 100
GenBank Accession No. CP030041

The CAZy database (www.cazy.org) was used to analyze carbohydrate-active enzymes (CAZymes) in the genome of strain MEBiC08714T. A total of predicted 323 CAZymes were identified, including these 187 glycosyl hydroxylase (GHs), 66 glycosyl transferases (GTs), 22 polysaccharide lyases (PLs), 13 carbohydrate esterases (CEs), and 35 carbohydrate-binding modules (CBMs) (Supplementary data Table S1). These findings were significantly higher than the sequenced strain Echinicolarosea JL3085 (Zhan et al., 2019) and other Bacteroidetes species (Tang et al., 2017). In additions, the genome contains CAZymes involved in the degradation of polysaccharides like agar (GH16), alginate (PL6 and PL17), carrageenan (GH16 and GH82), pectin (PL1 and PL10), starch (GH13), xylan (GH5, GH10, and GH30), and ulvan (PL40). The putative genes related to the polysaccharide regulation, uptake, and metabolism are often co-localized in the genomic loci of the phylum Bacteroidetes, and these loci are known as polysaccharide- utilization loci (PUL). PULDB (www.cazy.org/PULDB) predicted 90 PULs in the strain MEBiC08714T. The genome was found to contain PULs involved in the degradation of agar (β-agarase, DN752_04920), carrageenan (ι-carrageenanase, DN752_23580), pectin (pectate lyase, DN752_22275, DN752_23975), starch (α-amylase, DN752_20575), and xylan (xylanase, DN752_22450, DN752_23680, DN752_23685).

The putative genes encoding diverse polysaccharide-degrading enzymes of strain MEBiC08714T could be utilized as biological parts for engineering a metabolic pathway to produce oligosaccharides and biochemicals. Therefore, the genome of E. strongylocentroti MEBiC08714T provides fundamental genomic information for biotechnological applications in enzymatic polysaccharides conversion processes.

Strain and nucleotide sequence accession numbers

Echinicola strongylocentroti MEBiC08714T (MRS0020000 22798) was deposited to the Korean Collection for Type Cultures (KCTC 52052) and Japan Collection of Microorganisms (JCM 31307). The complete genome sequence of Echinicola strongylocentroti MEBiC08714T was deposited at DDBJ/EMBL/ GenBank under the accession CP030041.

적 요

Echinicola strongylocentroti MEBiC08714T은 성게(Strongylocentrotus intermedius)의 내장에서 분리되었으며, 한천, 알긴산, 카라기난 같은 다당류를 분해하는 특징이 있다. MEBiC08714T 균주의 유전체는 6,252,144 bp 크기로 4,695개의 코딩 서열을 포함하며 44.1 mol%의 GC 함량을 가진다. MEBiC08714T 균주는 187개의 glycosyl hydroxylases와 22개의 polysaccharide lyases을 포함한 많은 수의 탄수화물 활성 효소를 가지고 있다. 다양한 가수분해효소를 가지고 있는 E. strongylocentroti MEBiC08714T는 다당류의 효소 전환 공정에서 생물공학적 응용을 위한 후보로 사용될 수 있을 것이다.

Supplemental Materials
Acknowledgements

This work was supported by a grant from National Marine Biodiversity Institute of Korea (2019M00700).

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