基于比较基因组学分析大黄鱼来源波罗的海希瓦氏菌的防御系统

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

摘要:

【目的】波罗的海希瓦氏菌是冷藏海产品中常见的腐败菌，通过全基因组测序和转录组测序，分析它们的规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats，CRISPR)系统和限制修饰(restricted modification，R-M)系统，为波罗的海希瓦氏菌的基础生物学研究和海产品中微生物的致腐机制提供理论基础。【方法】分析大黄鱼来源波罗的海希瓦氏菌SB-19株和W-3株的致腐能力，对W-3株的全基因组序列进行测序、组装和注释，结合已报道的SB-19株和27株希瓦氏菌的全基因组序列，采用比较基因组学方法探究它们的CRISPR和R-M系统的差异，进而对SB-19株和W-3株在不同生长时期进行转录组测序，以及两株菌内致腐相关基因的共进化分析。【结果】灭菌大黄鱼汁中产生挥发性盐基总氮和三甲胺值显示波罗的海希瓦氏菌SB-19株和W-3株分别为强致腐能力和弱致腐能力菌株；平均核苷酸一致性证实SB-19株和W-3株为波罗的海希瓦氏菌，但基于全基因组构建的系统发育树则发现二者之间存在遗传信息上的差异；SB-19株具有相对完善的CRISPR系统，而W-3株则有更丰富的R-M系统；转录组测序反映出SB-19株在对数期和平台期的生长阶段具有更为活跃的新陈代谢能力和环境适应能力；但是这2株细菌中与致腐相关基因在进化过程中较为保守。【结论】CRISPR系统和R-M系统为异养型的波罗的海希瓦氏菌提供了较好的异源遗传信息入侵屏障，在维持物种遗传稳定性方面发挥了重要作用，但不参与该菌致腐能力差异的进化过程

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.