Integration of transcriptomic and proteomic analyses of cold shock response in Kosmotoga olearia, a typical thermophile with an incredible minimum growth temperature at 20 °C

Abstract

Kosmotoga olearia TBF 19.5.1 is a typical thermophile with optimal growth at 65 °C and also exhibits visible growth at an incredible minimum temperature (20 °C). It is considered an ideal model for investigating the evolutionary transition from thermophiles to mesophiles within Thermotogae. However, knowledge relevant to molecular mechanisms of K. olearia responding to cold shock is still limited. In this study, transcriptomics and proteomics were integrated to investigate the global variations at the transcript and protein level during cold shock in K. olearia. As a result, total 734 differentially expressed genes and 262 differentially expressed proteins were identified. The cold-responsive genes and proteins were associated with signaling transduction, transcription, translation and repair, cell wall/membrane reconstruction, amino acid biosynthesis, and stress response. However, most genes and proteins, involved in carbon metabolism, fatty acid biosynthesis, and energy production, were repressed. This work provides the first integrative transcriptomics and proteomics analyses of the cold shock response in K. olearia, and it offered new insights into the mechanisms of cold adaptation and post-transcriptional regulation of the distinctive thermophile within Thermotogae.

Keywords: Cold shock; Kosmotoga olearia; Proteomics; Transcriptomics.

Fig. 1

Growth profiles of K. olearia. A Growth curve of separate cultures maintained at 65 °C and 35 °C, respectively. B Growth curve of K. olearia at 65 °C and under cold shock at 35 °C. The data were shown as means ± SD (n = 3)

Fig. 2

Expression level and COG functional annotation in KOLCS vs KOL65. A The volcano figure of DEGs. B COG category distribution of DEGs. C The volcano figure of DEPs. D COG category distribution of DEPs. Red spots denoted up-regulated genes/proteins, green spots denoted down-regulated genes/proteins, and blue spots denoted no differentially expressed genes/proteins in volcano figure. Y-axis represented the number of genes/proteins, the bars at the top of the zero level indicated up-regulated genes/proteins, and the bars at the bottom represented down-regulated genes/proteins in COG distribution

Fig. 3

Validation of DEGs by RT-qPCR. Comparison of RNA-seq and RT-qPCR in expression changes of cspA, dnaK, rplL, groES, padR, fabH, cstA, and fabD. Log2 fold changes of transcript levels were determined with both measures (y-axis), and the data in RT-qPCR were shown as means ± SD (n = 3)

Fig. 4

Correlation analysis of all correlated proteins and transcripts (A), correlated DEPs and DEGs (B), and DEPs and DEGs with the same trend (C) based on the relative abundance log2 (KOLCS/KOL65) of proteome and transcriptome. Red dots represented DEPs and DEGs, green dots represented DEPs and non-DEGs, blue dots represented non-DEPs and DEGs, and purple blue dots represented non-DEPs and non-DEGs

Fig. 5

Overview of representative pathways influenced by cold shock via integrative analysis of transcriptome and proteome. Red and green colors indicated up- and down-regulated DEGs/DEPs, respectively

Fig. 6

Overview of the key gene and protein changes associated with the biosynthesis of lysine, arginine, and spermine under cold stress. Solid box represented differentially expressed genes, and empty box represented differentially expressed proteins. Red and blue represented up-regulation and down-regulation, respectively. The numbers indicated the fold changes in DEGs or DEPs