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Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH - Gut Pathog (2016)

Bottom Line: MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins.Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum.The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea ; Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju, 363-951 Republic of Korea.

ABSTRACT

Background: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution.

Results: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569).

Conclusions: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

No MeSH data available.


Related in: MedlinePlus

Comparative map of lateral flagella in NCCP15738 genome and other closely related species. Nine genes were highly conserved in 11 strains, but only seven genes (1–6, and 9) were conserved in NCCP15738. Numbers indicate genes encoding for the following proteins: flagellar hook protein FlgE, flagellar basal-body rod protein FlgF and FlgG from left to right (1); FlgD (2); FlgH (3); FlgA (4); FlgI (5); FlgC (6); FlgB (7); FlgK (8); FlgL (9); hypothetical protein (10); hypothetical protein (11); lysine-N-methylase (EC 2.1.1.-) (12); hypothetical protein (13); LfgM (14); membrane-bound lytic murein transglycosylase D precursor (EC 3.2.1.-) (15); MutT/nudix family protein (16); hemolysin (17); Cps2A (18); hypothetical protein (19); putative flagellin (20); hypothetical protein (21); glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) (22); LfgN (23); FlgJ (24 and 25). Gray background boxes indicate that the genes in the relative position are conserved in at least four species. The comparative map was created with the genome browser of the SEED viewer (version 2.0)
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Fig3: Comparative map of lateral flagella in NCCP15738 genome and other closely related species. Nine genes were highly conserved in 11 strains, but only seven genes (1–6, and 9) were conserved in NCCP15738. Numbers indicate genes encoding for the following proteins: flagellar hook protein FlgE, flagellar basal-body rod protein FlgF and FlgG from left to right (1); FlgD (2); FlgH (3); FlgA (4); FlgI (5); FlgC (6); FlgB (7); FlgK (8); FlgL (9); hypothetical protein (10); hypothetical protein (11); lysine-N-methylase (EC 2.1.1.-) (12); hypothetical protein (13); LfgM (14); membrane-bound lytic murein transglycosylase D precursor (EC 3.2.1.-) (15); MutT/nudix family protein (16); hemolysin (17); Cps2A (18); hypothetical protein (19); putative flagellin (20); hypothetical protein (21); glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) (22); LfgN (23); FlgJ (24 and 25). Gray background boxes indicate that the genes in the relative position are conserved in at least four species. The comparative map was created with the genome browser of the SEED viewer (version 2.0)

Mentions: A comparison of NCCP15738 genes and those of the two reference strains, E. coli K-12 substr. MG1655 and E. coli O157:H7 str. EDL933 showed that most of the functional genes of NCCP15738 were conserved in the two reference strains, but 941 genes were unique (Additional file 2: Table S2). Unique genes in NCCP15738 included those encoding lysis protein S, a two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal ion binding proteins, explain the phenotypic differences that result from environmental adaptation. In particular, NCCP15738 has a dual flagella system used for swarming in viscous media. This system resembles those found in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum [35]. Sixty-five genes encoded the flagellar biosynthesis protein or the flagellar structural protein. Seven of the flagella-related proteins (1–6, and 9) were highly conserved in V. parahaemolyticus and in nine other strains (Fig. 3, Additional file 3: Table S3). Lateral flagella have no effect on pathogenicity, but the polar flagellum is important in the pathogenesis of V. parahaemolyticus [36]. Therefore, we can suppose that the polar flagellum of NCCP15738 is the major machinery for swarming and has a pathogenic effect. In contrast, the lateral flagellum of NCCP15738 is likely related only to locomotion in this strain.Fig. 3


Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH - Gut Pathog (2016)

Comparative map of lateral flagella in NCCP15738 genome and other closely related species. Nine genes were highly conserved in 11 strains, but only seven genes (1–6, and 9) were conserved in NCCP15738. Numbers indicate genes encoding for the following proteins: flagellar hook protein FlgE, flagellar basal-body rod protein FlgF and FlgG from left to right (1); FlgD (2); FlgH (3); FlgA (4); FlgI (5); FlgC (6); FlgB (7); FlgK (8); FlgL (9); hypothetical protein (10); hypothetical protein (11); lysine-N-methylase (EC 2.1.1.-) (12); hypothetical protein (13); LfgM (14); membrane-bound lytic murein transglycosylase D precursor (EC 3.2.1.-) (15); MutT/nudix family protein (16); hemolysin (17); Cps2A (18); hypothetical protein (19); putative flagellin (20); hypothetical protein (21); glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) (22); LfgN (23); FlgJ (24 and 25). Gray background boxes indicate that the genes in the relative position are conserved in at least four species. The comparative map was created with the genome browser of the SEED viewer (version 2.0)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4835932&req=5

Fig3: Comparative map of lateral flagella in NCCP15738 genome and other closely related species. Nine genes were highly conserved in 11 strains, but only seven genes (1–6, and 9) were conserved in NCCP15738. Numbers indicate genes encoding for the following proteins: flagellar hook protein FlgE, flagellar basal-body rod protein FlgF and FlgG from left to right (1); FlgD (2); FlgH (3); FlgA (4); FlgI (5); FlgC (6); FlgB (7); FlgK (8); FlgL (9); hypothetical protein (10); hypothetical protein (11); lysine-N-methylase (EC 2.1.1.-) (12); hypothetical protein (13); LfgM (14); membrane-bound lytic murein transglycosylase D precursor (EC 3.2.1.-) (15); MutT/nudix family protein (16); hemolysin (17); Cps2A (18); hypothetical protein (19); putative flagellin (20); hypothetical protein (21); glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) (22); LfgN (23); FlgJ (24 and 25). Gray background boxes indicate that the genes in the relative position are conserved in at least four species. The comparative map was created with the genome browser of the SEED viewer (version 2.0)
Mentions: A comparison of NCCP15738 genes and those of the two reference strains, E. coli K-12 substr. MG1655 and E. coli O157:H7 str. EDL933 showed that most of the functional genes of NCCP15738 were conserved in the two reference strains, but 941 genes were unique (Additional file 2: Table S2). Unique genes in NCCP15738 included those encoding lysis protein S, a two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal ion binding proteins, explain the phenotypic differences that result from environmental adaptation. In particular, NCCP15738 has a dual flagella system used for swarming in viscous media. This system resembles those found in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum [35]. Sixty-five genes encoded the flagellar biosynthesis protein or the flagellar structural protein. Seven of the flagella-related proteins (1–6, and 9) were highly conserved in V. parahaemolyticus and in nine other strains (Fig. 3, Additional file 3: Table S3). Lateral flagella have no effect on pathogenicity, but the polar flagellum is important in the pathogenesis of V. parahaemolyticus [36]. Therefore, we can suppose that the polar flagellum of NCCP15738 is the major machinery for swarming and has a pathogenic effect. In contrast, the lateral flagellum of NCCP15738 is likely related only to locomotion in this strain.Fig. 3

Bottom Line: MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins.Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum.The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea ; Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju, 363-951 Republic of Korea.

ABSTRACT

Background: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution.

Results: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569).

Conclusions: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

No MeSH data available.


Related in: MedlinePlus