DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection. (February 2019)

• Record Type: Journal Article
• Authors: Hu, Lijun; Stones, Robert; Brown, Eric W.; Allard, Marc W.; Ma, Li M.; Zhang, Guodong
• Is Part Of: Food control. Volume 96(2019)
• Page Start: 271
• Page End: 280
• Publication Date: 2019-02
• Subjects: prot6E -- sefA -- Enteritidis -- WGS -- Protein structure; Food -- Quality -- Periodicals; Food -- Analysis -- Periodicals; Food handling -- Periodicals; Food industry and trade -- Quality control -- Periodicals; Aliments -- Industrie et commerce -- Qualité -- Contrôle -- Périodiques; Aliments -- Qualité -- Périodiques; Aliments -- Analyse -- Périodiques; Hygiène alimentaire -- Périodiques; Food -- Analysis; Food handling; Food -- Quality; Periodicals; Electronic journals; 664.07
• DOI: 10.1016/j.foodcont.2018.09.018
• Languages: English
• ISSNs: 0956-7135

Abstract

Abstract: Genes prot 6E and sef A are used as targets for detection of Salmonella enterica subsp. enterica serovar Enteritidis ( Salmonella ser. Enteritidis). We investigated variations in these genes across 64 different Salmonella ser. Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. Isolates were sequenced using Illumina technologies. Based on the resulting phylogenetic tree, our isolates clustered in 2 distinct clades. All isolates carried prot 6E and sef A. Comparative genomic analyses indicated two non-synonymous mutations (Glycine → Serine and Valine → Isoleucine) of prot 6E in 11 isolates (9 egg samples, 2 chicken samples). However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. We identified one non-synonymous mutation (Valine → Glutamic Acid) in the sef A gene in 4 isolates from egg samples. The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. Enteritidis isolates revealed prot6 E gene was located on the tail of the plasmid. Based on the biosynthesis of amino acids - Reference pathway in the KEGG pathway Database, the transition of amino acid from sef A Var. was a transversion from essential amino acid to non-essential amino acid, while that of prot 6E Var.1 happened between the conditionally non-essential amino acid, and prot 6E Var. 2 occurred between essential amino acids. Properties of these mutated amino acids, such as side-chain polarity or charge, may contribute to the occurrence and rate of mutations in prot 6E and sef A. These insights can be used to improve detection methods for Salmonella ser. Enteritidis.