Transcriptomic time-series analysis of cold and heat shock response in psychrotrophic lactic acid bacteria

Background:Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in cold stored modified atmosphere packaged food product microbiota and they are the main cause of food spoilage. But still, the cold- and heat-shock response of the spoilage related psychrotrophic lactic acid bacteria has not been well studied. Here, to study cold- and heat-shock response of spoilage lactic acid bacteria, we performed time-series RNA-seq for Le. gelidum, Lc. piscium and P. oligofermentans using temperatures of 0 °C, 4°C, 14°C, 25°C and 28°C.Results:We showed that the cold-shock protein A (CspA) gene was upregulated during cold-shock treatment, meaning only CspA is responsible for cold shock response among cold-shock protein genes in all three species. Our results indicated DEAD-box RNA helicase genes (cshA, cshB) play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNAase genes were also involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species was a strong indication that these genes were part of cold-shock response. Heat-shock treatment caused upregulation of protein folding genes in all three species and we were able to show transcription binding site motif for heat-shock response genes in Le. gelidum, Lc. piscium. Finally, we showed that spoilage related genes were upregulated during cold temperature.Conclusions:The results of this study provide new insights into a better understanding of the cold- and heat-shock response in psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as a target for future studies.