Study On Heat Stress Response Process Of Escherichia Coli Based On Transcriptome

Life systems exist in complex environmental contexts.To adapt to environment change,organisms need to adjust their established steady states by sensing and response.Temperature is an important aspect of environmental conditions.The adaptation mechanisms of living organisms to temperature change have always been one of the hotspots in life science,and the research achievements have been widely used in many fields such as genetic engineering,fermentation engineering,enzyme engineering and new biological materials.However,the internal molecular mechanisms of heat stress response of living organisms are still not quite clear for now.In this work,transcriptomic datasets reflecting the states of optimal growth and heat stress of E.coli were produced by RNASeq,and the heat stress response process of E.coli was explored by analyzing gene expression profiles and corresponding protein-protein interaction networks(PPINs).Firstly,we refined the culture medium based on previous research experiences and pre-experiments,improved the procedure of heat stress experiment for E.coli,and determined the sampling time points for RNA-Seq of E.coli in batch culture in the states of optimal growth and heat stress by physiological experiments.Then,we performed strand-specific sequencing for the RNA samples and obtained the transcriptome data of different growth stages under the optimal and heat stress experimental conditions,respectively.Based on the gene expression profiles,differentially expressed genes(DEGs)between the states of optimal growth and heat stress were identified and analyzed;the results showed that the number of up-regulated genes is significantly increased in the heat stress stage compared with the heat shock stage.The results of GO function enrichment analysis and KEGG pathway enrichment analysis of the DEGs showed that in the heat shock stage,normal physiological activity is inhibited,energy metabolism is suppressed,heat shock response is active,misfolded proteins are degraded into amino acids used for synthesizing heat shock proteins,and the cells are in a typical stringent state;while in the heat stress stage,heat shock response is wear off,some suppressed physiological functions under heat shock are recovered,some silenced genes under optimal growth condition are activated and related metabolic pathways are operating,which implies that the cells are in a new steady state in the heat stress stage compared with the optimal growth state.Then the PPINs for the DEGs were reconstructed and the hub nodes in the PPINs were selected out and analyzed.The modules in the PPINs were obtained by using MCL clustering algorithm and the results showed that most of the physiological activities involved in the heat adaptation process are performed by functional modules of proteins,and proteins with similar physiological functions tend to be enriched in the same functional module.Furthermore,function analysis of the PPIN hub nodes and the functional enrichment analysis for the components of PPIN modules also support the conclusions obtained based on the corresponding analysis of transcriptome.At last,PPINs reflecting optimal growth and heat stress states were reconstructed,and their topological properties were calculated and compared.The results showed that the differences of the topological properties are very small between the two physiological states,indicating the robustness of the structure and function of the PPIN.Based on the results of this research,the selection mechanism of the adaptation strategies in the heat stress response process was speculated by employing the concept of "potential barrier" in physics.This work provided experiment protocol and research direction for the subsequent studies of the heat stress response of E.coli,and laid a foundation for further revealing the internal selection mechanisms of adaptation strategies of living organisms.