Comparative genomics of defense system in Shewanella baltica isolated from large yellow croaker

Abstract:

[Objective]Shewanella baltica is a specific spoilage organism commonly foundin seafood during cold storage. To figure out the defense system of S.baltica isolated from large yellow croaker (Pseudosciaena crocea), we analyzed the clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification (R-M) system of this bacterium, aiming to provide a theoretical basis for the research on S.baltica and the spoilage mechanism of seafood. [Methods] The spoilage abilities of S.baltica strains SB-19 and W-3 were determined. The whole-genome sequences of the two strains were compared with 27 Shewanella strains, and their CRISPRs and R-M system were analyzed through comparative genomics tools. Finally, the transcriptomes of SB-19 and W-3 strains in different growth phases were sequenced, and the coevolution of spoilage-related genes in the two strains was analyzed. [Results] The total volatile basic nitrogen and trimethylamine produced in the sterilized fish juice showed that the SB-19 and W-3 had strong and weak spoilage abilities, respectively. The values of average nucleotide identity confirmed that both SB-19 and W-3 were S.baltica, while the phylogenetic tree based on the whole genomes showed genetic differences between them. SB-19 had a complete CRISPR system, while W-3 had an abundant R-M system. Transcriptome sequencing results indicated that SB-19 had more active metabolism and environmental adaptability in the logarithmic phase and stationary phase. The spoilage-related genes in these two strains were relatively conserved during evolution. [Conclusion]The CRISPRs and R-M system in heterotrophic S.baltica provide a good barrier against the invasion of heterologous genetic information and play a role in maintaining the genetic stability of species. However, they are not involved in the evolutionary process of the spoilage ability differences between S.baltica strains.