Genomic Insights and Its Comparative Analysis with Yersinia enterocolitica Reveals the Potential Virulence Determinants and Further Pathogenicity for Foodborne Outbreaks원문보기
Yersinia enterocolitica is a well-known foodborne pathogen causing gastrointestinal infections worldwide. The strain Y. enterocolitica FORC_002 was isolated from the gill of flatfish (plaice) and its genome was sequenced. The genomic DNA consists of 4,837,317 bp with a GC content of 47.1%, and is pr...
Yersinia enterocolitica is a well-known foodborne pathogen causing gastrointestinal infections worldwide. The strain Y. enterocolitica FORC_002 was isolated from the gill of flatfish (plaice) and its genome was sequenced. The genomic DNA consists of 4,837,317 bp with a GC content of 47.1%, and is predicted to contain 4,221 open reading frames, 81 tRNA genes, and 26 rRNA genes. Interestingly, genomic analysis revealed pathogenesis and host immune evasion-associated genes encoding guanylate cyclase (Yst), invasin (Ail and Inv), outer membrane protein (Yops), autotransporter adhesin A (YadA), RTX-like toxins, and a type III secretion system. In particular, guanylate cyclase is a heat-stable enterotoxin causing Yersinia-associated diarrhea, and RTX-like toxins are responsible for attachment to integrin on the target cell for cytotoxic action. This genome can be used to identify virulence factors that can be applied for the development of novel biomarkers for the rapid detection of this pathogen in foods.
Yersinia enterocolitica is a well-known foodborne pathogen causing gastrointestinal infections worldwide. The strain Y. enterocolitica FORC_002 was isolated from the gill of flatfish (plaice) and its genome was sequenced. The genomic DNA consists of 4,837,317 bp with a GC content of 47.1%, and is predicted to contain 4,221 open reading frames, 81 tRNA genes, and 26 rRNA genes. Interestingly, genomic analysis revealed pathogenesis and host immune evasion-associated genes encoding guanylate cyclase (Yst), invasin (Ail and Inv), outer membrane protein (Yops), autotransporter adhesin A (YadA), RTX-like toxins, and a type III secretion system. In particular, guanylate cyclase is a heat-stable enterotoxin causing Yersinia-associated diarrhea, and RTX-like toxins are responsible for attachment to integrin on the target cell for cytotoxic action. This genome can be used to identify virulence factors that can be applied for the development of novel biomarkers for the rapid detection of this pathogen in foods.
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대상 데이터
enterocolitica were also present (Ail, Inv, Yst, TTSS, Yops, siderophore receptor, and RTX toxins) in the genome of strain FORC_002 and corresponded with its identity as a pathogen [49]. The GIs were identified in the genome of strain FORC_002, which includes a novel TTSS, Yersinia secretion apparatus (Ysa), an ATP binding transporter system, an insecticidal toxin complex (TC) cluster, an RTX toxin cluster, a colicin E6 immunity protein cluster, a flagellum gene cluster, a respiration control protein (arcA), and six prophage-related genes. The genome also has putative VFs such as novel TTSS, RTX-like toxin, and Yst (heat labile enterotoxin) in genomic pathogenicity islands, and this suggests that strain FORC_002 regulates host gene expression during infection in humans and animals.
The plasmid pFORC2 (Fig. 3B) consists of 101,782 bp with a GC content of 42.8% and a total of 105 predicted ORFs. Among the predicted ORFs, almost 48 ORFs (46%) were annotated as hypothetical genes, and the remaining 57 ORFs (54%) were assigned as functional genes.
이론/모형
All complete genome sequences of Y. enterocolitica strains were obtained from the NCBI Genome database (http://www.ncbi. nlm.nih.gov/genome/genomes/1041) and their ANI value was calculated using the unweighted pair group method. ANI was calculated between two genomes, where the query genome was spliced into 1,020 nucleotide fragments, each of which was blasted against the subject genome [40].
The tree uses sequences aligned by ClustalW, uses the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. Phylogenetic analyses were performed using MEGA6 [58]. The building of the tree also involves a bootstrapping process repeated 1,000 times to generate a majority consensus tree.
To identify the closest genome sequences, the genome tree was constructed using R software [41] based on ANI values. The genomic islands (GIs) were identified using the SIGI-HMM algorithm in Colombo ver. 3.8 [42]. The genome properties of strain FORC_002 were compared with published genomes of strains 8081, 105.
enterocolitica FORC_002 as being related to other type strains within the genus Yersinia. The tree uses sequences aligned by ClustalW, uses the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. Phylogenetic analyses were performed using MEGA6 [58].
성능/효과
8% and a total of 105 predicted ORFs. Among the predicted ORFs, almost 48 ORFs (46%) were annotated as hypothetical genes, and the remaining 57 ORFs (54%) were assigned as functional genes. The virulence plasmid pYV encodes many virulence genes (ssa, lcr, virF, Grx2, and arsA) essential for defense against the host and resistance to heavy metals.
The whole genome comprises a total of 4,131 predicted ORFs, 81 tRNA genes, and 26 rRNA genes (Table 3). Among the predicted ORFs, almost one-fourth of genes (22%) were annotated as hypothetical or uncharacterized genes (890 ORFs), and the majority of the remaining genes (78%) were assigned as functional genes (3,241 ORFs). Analysis of COG functional categorization predicted that 3,653 COGs (81%) encoded known functional proteins, whereas 837 COGs (19%) were of unknown function.
Among the predicted ORFs, almost one-fourth of genes (22%) were annotated as hypothetical or uncharacterized genes (890 ORFs), and the majority of the remaining genes (78%) were assigned as functional genes (3,241 ORFs). Analysis of COG functional categorization predicted that 3,653 COGs (81%) encoded known functional proteins, whereas 837 COGs (19%) were of unknown function.
enterocolitica are unique, highly similar, and evolved from a common ancestor. Another phylogenetic tree was constructed based on the ANI value to compare the complete genome sequence of strain Y. enterocolitica FORC_002 with other strains of Y. enterocolitica (8081, 105.5R, Y11, WA, 2516-87, and LC20). These results indicate that the genome of 8 081 and WA showed the h ighest identity with s train FORC_002 with an ANI value of 96.
enterocolitica. The phylogenetic result indicates that all foodborne strains of Y. enterocolitica are highly similar and may have evolved from a common ancestor.
5R, Y11, WA, 2516-87, and LC20). These results indicate that the genome of 8 081 and WA showed the h ighest identity with s train FORC_002 with an ANI value of 96.3% (Fig. 4), and the lowest identity with LC20 (85.95%). Other Y.
analysis of the 16S rRNA gene indicates that strain FORC_002 shares over 99% sequence identities with all other strains of Y. enterocolitica, and 96-98% sequence identities with other species of Yersinia. The 16S rRNA sequence of strain FORC_002 showed the highest sequence identities (>99%) with the species strains of Y.
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