Genomic Analysis of the Extremely Halophilic Archaeon Halobacterium noricense CBA1132 Isolated from Solar Salt That Is an Essential Material for Fermented Foods원문보기
Lim, Seul Ki
(Microbiology and Functionality Research Group, World Institute of Kimchi)
,
Kim, Joon Yong
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Song, Hye Seon
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Kwon, Min-Sung
(Microbiology and Functionality Research Group, World Institute of Kimchi)
,
Lee, Jieun
(Microbiology and Functionality Research Group, World Institute of Kimchi)
,
Oh, Young Jun
(Microbiology and Functionality Research Group, World Institute of Kimchi)
,
Nam, Young-Do
(Research Group of Gut Microbiome, Korea Food Research Institute)
,
Seo, Myung-Ji
(Division of Bioengineering, Incheon National University)
,
Lee, Dong-Gi
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Choi, Jong-Soon
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Yoon, Changmann
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Sohn, Eunju
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Rahman, MD. Arif-Ur
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Roh, Seong Woon
(Biological Disaster Analysis Group, Korea Basic Science Institute)
,
Choi, Hak-Jong
(Microbiology and Functionality R)
The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. St...
The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.
The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.
For phylogenetic analysis, three phylogenetic trees were constructed based on the 16S rRNA gene, five housekeeping genes for multilocus sequence typing (MLST), and average nucleotide identity (ANI). The 16S rRNA gene sequence of strain CBA1132 was extracted from the genome sequences using the RNAmmer 1.
Genomic DNA was extracted using a QuickGene DNA tissue kit S (Kurabo) and purified using an MG Genomic DNA purification kit (Doctor Protein) according to the manufacturers’ instructions. Genomic DNA of strain CBA1132 was sequenced using next-generation sequencing technology (PacBio RS II system; Pacific Biosciences) according to the manufacturer’s instructions and was assembled using PacBio SMRT Analysis 2.3.0 (Pacific Biosciences). The genome sequence of stain CBA1132 was deposited in the DDBJ under the accession numbers BCMZ01000001–BCMZ01000004.
대상 데이터
The cell morphology of CBA1132 and examination for contamination by other microorganisms were detected using a light microscope (ECLIPSE 80i; Nikon). The strain has been deposited at the Korean Culture Center of Microorganisms (KCCM) and Japan Collection of Microorganisms (JCM) under accession number KCCM 43183 and JCM 31150, respectively.
이론/모형
Phylogenetic relationships between strain CBA1132 and its most closely representative species were determined using the MEGA6 software [44]. Phylogenetic consensus trees were constructed using the neighbor-joining (NJ) [38], maximum-parsimony (MP) [20], and maximum-likelihood (ML) [13] methods with 1,000 randomly selected bootstrap replicates. The phylogenetic tree based on ANI values was constructed using CLgenomics ver.
Five different housekeeping genes were used to generate the MLST phylogenetic tree: V-type ATP synthase subunit B (atpB), elongation factor 2 (EF-2), DNA repair and recombination protein RadA (radA), DNA-directed RNA polymerase subunit beta (rpoB´), and protein translocase subunit SecY (secY). The 16S rRNA gene sequences and concatenated amino acid sequences inferred from the five genes for MLST were aligned with those of the most closely related species, respectively, using the multiple alignment program ClustalW [45]. Phylogenetic relationships between strain CBA1132 and its most closely representative species were determined using the MEGA6 software [44].
성능/효과
As summarized in Table 2 and visualized in Fig. 1, the genome contained 3,208 open reading frames (ORFs), 3,084 coding sequences (CDS), three rRNA genes (5S, 16S, and 23S), and 44 tRNA genes. The genomic G + C content was 65.
salinarum R1) shown in Figs. 2B and 2C indicated that strain CBA1132 and strain DL1 cluster separately to strains NRC-1 and R1, suggesting that strains CBA1132 and DL1 are more closely related than the other two strains.
95%. A total of 2,536 genes were analyzed based on the COG functional categories (http://www.ncbi.nlm.nih.gov/COG/): 159 genes in energy production, 72 in carbohydrate transport and metabolism, 213 in amino acid transport and metabolism, 62 in nucleotide transport and metabolism, and 99 in coenzyme transport and metabolism (Table 3). Based on the RAST pipeline, metal resistance-associated genes coding copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR) were annotated.
gov/COG/): 159 genes in energy production, 72 in carbohydrate transport and metabolism, 213 in amino acid transport and metabolism, 62 in nucleotide transport and metabolism, and 99 in coenzyme transport and metabolism (Table 3). Based on the RAST pipeline, metal resistance-associated genes coding copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR) were annotated. The ars operon is required for the detoxification of arsenate and arsenite.
In the genus Halobacterium clade, each branch was conserved on the basis of not only NJ algorithm but also MP and ML algorithms. Moreover, high bootstrap values indicated that strain CBA1132 belongs to the genus Halobacterium. The phylogenetic trees based on MLST genes and ANI with the three reported strains in genus Halobacterium (Hbt.
Colonies of strain CBA1132 were circular and pink in colour, and coccoid form of the cells was observed. The draft genome sequence of strain CBA1132 comprised of four contigs, with a genome size of 3,012,807 bp and an N50 of 2,587,453 bp. As summarized in Table 2 and visualized in Fig.
1, the genome contained 3,208 open reading frames (ORFs), 3,084 coding sequences (CDS), three rRNA genes (5S, 16S, and 23S), and 44 tRNA genes. The genomic G + C content was 65.95%. A total of 2,536 genes were analyzed based on the COG functional categories (http://www.
salinarum R1. The result of the whole genome alignment using Mauve, represented by the highly homologous regions with the locally collinear blocks, suggested that strain CBA1132 shows more genome rearrangements as compared with the other three genomes of genus Halobacterium (Fig. 3).
Through the gene prediction processes, metal resistance-associated genes were found in the genome of strain CBA1132. These results indicate that strain CBA1132 might be able to survive at high concentrations of metal ions. Nitrogen is an essential and major element in all organisms; the nitrogen-cycle metabolic pathway has been studied widely in Bacteria, Eukarya, and Archaea [3, 4].
후속연구
Further studies of the genome sequence of Hbt. noricense CBA1132 will be useful for potential commercial applications, using the haloarchaeal extremozymes and their physiological functionality, and for future molecular biological studies.
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