Complete genome sequence of Altibacter species strain ALE3EI isolated from Jeju Island

(1)

Here we report complete genome sequence of Gram-negative, rod-shaped, and chemoheterotrophic aerobic bacterial strain ALE3EI. The 16S rRNA gene sequence analysis revealed that strain ALE3EI showed high similarity with the Altibacter lentus JLT2010

^T

(96.7% similarity). Altibacter sp. ALE3EI had a circular chromosome of 2,987,299 bp with 40.38% G + C content. Total genes of 2,729 in number were predicted: 2,654 protein coding genes, 2 rRNA operons, and 37 tRNA genes could be assigned. Canonical glycolytic and pentose phosphate pathways were present. In addition to two proteases and one protease inhibitor, the genome harbors the genes for synthesis and degradation of cyanophycin, which is a nitrogen-storage polymer composed of a polyaspartate backbone with arginine side chains and is of biomedical interest as a biodegradable substitute for synthetic polyacrylates.

Keywords: ALE3EI, Altibacter, complete genome, cyanophycin

Gram-negative, rod-shaped, non-motile, and chemohetero- trophic, Altibacter sp. ALE3EI was isolated from a volcanic aquifer of Jeju Island, Republic of Korea (N 33.5327, E 126.

8204). Strain ALE3EI formed carotenoid-colored colonies

when isolated and pure-cultured on Marine Agar 2216. The 16S rRNA gene sequence analysis revealed that strain ALE3EI showed high similarity with the Altibacter lentus JLT2010

^T

(96.7%) (unpublished data).

Here we report the complete genome analysis of the Altibacter sp. ALE3EI using single-molecule real-time technology (SMRT).

The complete genome of strain ALE3EI was obtained using PacBio RS II single-molecule real-time sequencing technology (Pacific Biosciences). Library with an average of 20 kb inserts was prepared yielding > 352.84 × average genome coverage and de novo assembly of the 112,619 reads with an average of 14,158 nucleotides was carried out (1,594,478,562 bp in total) using the hierarchical genome-assembly process pipeline of the SMRT Analysis version 2.3.0 with default parameters (Chin et al., 2013). Functional annotations of the predicted coding sequences are as in our previous publication (Oh et al., 2019).

The genome of Altibacter sp. strain ALE3EI consists of one circular chromosome of 2,987,299 bp with 40.38% G + C content (Table 1). A total of 2,729 genes were predicted in the genome of this strain, 2,654 of which are protein coding genes.

2,061 of protein coding genes were functionally assigned, while the rest of genes were annotated as hypothetical proteins.

The chromosome harbors 2 rRNA operons (made up of 5S,

Korean Journal of Microbiology (2020) Vol. 56, No. 4, pp. 387-389 pISSN 0440-2413

DOI https://doi.org/10.7845/kjm.2020.0079 eISSN 2383-9902

Complete genome sequence of Altibacter species strain ALE3EI isolated from Jeju Island

Hyun-Myung Oh

¹

, Dongil Jang

²

, and Myung Won Lee

³

*

1

Institute of Liberal Arts Education, Pukyong National University, Busan 48547, Republic of Korea

2

Cotde, Inc., Cheonan 31252, Republic of Korea

3

Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea

제주도에서 분리된 Altibacter species strain ALE3EI의 완성 유전체 서열

오현명

¹

･ 장동일

²

･ 이명원

³

*

1

부경대학교 기초교양교육원,

²

주식회사 콧데,

³

부경대학교 화학과

(Received August 18, 2020; Revised September 22, 2020; Accepted September 24, 2020)

*For correspondence. E-mail: mwlee@pknu.ac.kr;

Tel.: +82-51-629-5590; Fax: +82-51-629-5583

(2)

388

^∙ ^Ohet al.

미생물학회지 제56권 제4호

16S, and 23S rRNA genes with an additional 5S gene) and 37 tRNA genes (Table 1). Neither CRISPR nor prophage loci were found on the completed genome of strain ALE3EI.

Strain ALE3EI harbors full gene sets for glycolysis, TCA cycle, and pentose phosphate pathway. The genes for hydro- lyzing polysaccharides such as starch, chitin, cellulose, and fucoidan were not identified. Additional genes for utilizing disaccharides such as sucrose and lactose were not identified, but two copies of gene for mannose utilization, i.e., mannose-6- phosphate isomerases that may convert mannose to fructose-6- phosphate, were identified (ALE3EI_1115 and ALE3EI_1727).

It indicates that Altibacter sp. could only utilize monosac-

charides including glucose, fructose, and mannose as carbon sources. The strain contains most of the genes related to de novo synthesis pathway for DNA building blocks and essential amino acids, except the genes for branched-chain amino acids from pyruvate; L-isoleucine, L-valine, and L-leucine.

Using MEROPS database (Rawlings et al., 2018), the gene for zinc metalloprotease (ALE3EI_1920) that cleaves extracel- lular matrix proteins such as elastin and keratin was found. In an operon with pbp1C (ALE3EI_1013) for penicillin-binding protein 1C, broad-spectrum inhibitor of protease, alpha-2- macroglobulin (α2M, ALE3EI_1014), was found. Pbp1C is bifunctional (i.e., transpeptidase and transglycosylase) and both functions are essential for the synthesis of the peptido- glycan layer.

The genome harbors the genes for cyanophycin synthase (ALE3EI_1198) and cyanophycinase (ALE3EI_1197) for synthesis and degradation of cyanophycin, a nitrogen-storage polymer composed of a polyaspartate backbone with arginine side chains. Cyanophycin is of biomedical interest as a bio- degradable substitute for synthetic polyacrylates (Hai et al., 2006; Mooibroek et al., 2007). Besides, the gene for soluble epoxide hydrolase/lipid-phosphate phosphatase (ALE3EI_1577) was identified.

Nucleotide sequence and strain accession number The complete genome sequence of Altibacter sp. ALE3EI has been deposited at DDBJ/EMBL/GenBank under the accession number CP052909. The strain is available from Cotde Inc. (daniel@cotde.co.kr) or from Japan Collection of Microorganisms (JCM 33022).

적 요

제주도 용암 해수 시료에서 분리 동정된 그람 음성 종속영 양 간균인 ALE3EI 균주는 표준 균주인 Altibacter lentus JLT 2010

^T

에 96.7%의 16S rRNA 서열 상동성을 가지고 있었다. 유 전체 서열 분석의 결과 원형의 세균 유전체는 그 길이가 2,987,299 bp였으며 40.38%의 G + C 비율을 가졌다. 전체 2,729개의 유 전자는 2,654개의 단백질을 코드하는 서열이며, 두 개의 rRNA 오페론과 37개의 tRNA 유전자를 가지고 있었다. 해당작용 및 5탄당인산염 대사 경로가 존재하였다. 두 개의 단백질 분해 효

Table 1. Altibacter sp. ALE3EI genome assembly and its general features

Item Description

Genome Assembly Data

Assembly Method SMRT Analysis v. 2.3.0 Genome Coverage 352.84 ×

Sequencing Technology PacBio RS II with P6-C4 chemistry MIGS Data

Investigation_type bacteria_archaea

Project_name Genome sequencing of Altibacter sp. ALE3EI

Lat_lon N33.5327, E126.8204

Depth NA

Alt_elev NA

Country South Korea: Jeju Island

Environment Seawater

Geo_loc_name South Korea Collection_date 2016-02-18

Env_biome ocean biome [ENVO:01000048]

Env_feature seawater [ENVO:00002149]

Env_material lava seawater

Ploidy haploid

Num_replicons 1

Extrachrom_elements NA Ref_biomaterial NA Source_mat_id ALE3EI Biotic_relationship free living Trophic_level chemoheterotroph Rel_to_oxygen aerobic

Isol_growth_condt NA

Sequencing_meth PacBio RS II sequencing Assembly SMRT Analysis v2.3.0

Finishing_strategy complete; 352.84× coverage; 1 contig Annot_source Prodigal v2.6.3

(3)

Complete genome sequence of Altibacter species strain ALE3EI∙

389 Korean Journal of Microbiology, Vol. 56, No. 4 소와 한 개의 단백질 분해 효소 저해제 외에 cyanophycin 생합

성과 분해를 하는 유전자가 존재하였다. 다중의 아스파르트산 의 주골격에 아르기닌 곁사슬을 가지는 질소 저장용 고분자 중합체인 cyanophycin은 의료용 소재로 활용 가능한 폴리아 크릴레이트의 생분해성 대체 물질이다.

Acknowledgments

This research was supported the National Research Foundation (NRF-2017R1D1A1B03034706).

References

Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. 2013.

Nonhybrid, finished microbial genome assemblies from long- read SMRT sequencing data. Nat. Methods 10, 563–569.

Hai T, Frey KM, and Steinbüchel A. 2006. Engineered cyanophycin synthetase (CphA) from Nostoc ellipsosporum confers enhanced CphA activity and cyanophycin accumulation to Escherichia coli. Appl. Environ. Microbiol. 72, 7652–7660.

Mooibroek H, Oosterhuis N, Giuseppin M, Toonen M, Franssen H, Scott E, Sanders J, and Steinbüchel A. 2007. Assessment of technological options and economical feasibility for cyanophycin biopolymer and high-value amino acid production. Appl.

Microbiol. Biotechnol. 77, 257–267.

Oh HM, Kim DH, Han SJ, Song JH, Kim K, and Jang D. 2019.

Complete genome sequence of Marinobacter salarius HL2708#2 isolated from a lava sea water en viron men t on Jeju Islan d.

Korean J. Microbiol. 55, 69–73.

Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, and Finn RD. 2018. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 46, D624–D632.