search for




 

Complete genome sequence of Altibacter species strain ALE3EI isolated from Jeju Island
Korean J. Microbiol. 2020;56(4):387-389
Published online December 31, 2020
© 2020 The Microbiological Society of Korea.

Hyun-Myung Oh1, Dongil Jang2, and Myung Won Lee3*

1Institute of Liberal Arts Education, Pukyong National University, Busan 48547, Republic of Korea
2Cotde, Inc., Cheonan 31252, Republic of Korea
3Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea
Correspondence to: E-mail: mwlee@pknu.ac.kr;
Tel.: +82-51-629-5590; Fax: +82-51-629-5583
Received August 18, 2020; Revised September 22, 2020; Accepted September 24, 2020.
Abstract
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 JLT2010T (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
Body

Gram-negative, rod-shaped, non-motile, and chemoheterotrophic, 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gene sequence analysis revealed that strain ALE3EI showed high similarity with the Altibacter lentus JLT2010T (96.7%) (unpublished data).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, 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.

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


Strain ALE3EI harbors full gene sets for glycolysis, TCA cycle, and pentose phosphate pathway. The genes for hydrolyzing 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 monosaccharides 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 extracellular 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 peptidoglycan 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 biodegradable 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 종속영양 간균인 ALE3EI 균주는 표준 균주인 Altibacter lentus JLT 2010T에 96.7%의 16S rRNA 서열 상동성을 가지고 있었다. 유전체 서열 분석의 결과 원형의 세균 유전체는 그 길이가 2,987,299 bp였으며 40.38%의 G + C 비율을 가졌다. 전체 2,729개의 유전자는 2,654개의 단백질을 코드하는 서열이며, 두 개의 rRNA 오페론과 37개의 tRNA 유전자를 가지고 있었다. 해당작용 및 5탄당인산염 대사 경로가 존재하였다. 두 개의 단백질 분해 효소와 한 개의 단백질 분해 효소 저해제 외에 cyanophycin 생합성과 분해를 하는 유전자가 존재하였다. 다중의 아스파르트산의 주골격에 아르기닌 곁사슬을 가지는 질소 저장용 고분자 중합체인 cyanophycin은 의료용 소재로 활용 가능한 폴리아크릴레이트의 생분해성 대체 물질이다.

Acknowledgments

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

References
  1. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, and Eichler EEEichler EE, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569.
    Pubmed CrossRef
  2. 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.
    Pubmed KoreaMed CrossRef
  3. 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.
    Pubmed KoreaMed CrossRef
  4. 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 environment on Jeju Island. Korean J. Microbiol. 55, 69-73.
  5. 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.
    Pubmed KoreaMed CrossRef


December 2020, 56 (4)
Full Text(PDF) Free

Social Network Service
Services

Author ORCID Information

Funding Information