Differential analysis of transcriptome of psychrophilic bacteria under different culture temperatures

Abstract

Background: Psychrophilic bacteria can survive in a unique living environment.

Objective: To explore the mechanism of low temperature adaptation and the physiological function of thermophilic metabolic genes.

Method: Serratia marcescens strain F13 stored in microbial laboratory was cultured at 5∘C, 10∘C and 25∘C respectively, and the obtained strains were sequenced by high-throughput transcriptome. Serratia marcescens strain CAV1761 was used as the reference strain. The data produced by transcriptome sequencing were statistically analyzed by biostatistics software such as soapnuke, soap and edger. The differentially expressed genes were found based on the gene expression, and analyzed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.

Results: The results showed that there were 718 differential genes in F13-10 vs F13-5 comparison group, 1614 differential genes in F13-25 vs F13-5 comparison group and 1636 differential genes in F13-25 vs F13-10 comparison group. GO function enrichment analysis showed that the GO term mainly enriched by different genes in the three comparison groups was mostly related to the migration and transport of cellular or subcellular components, cell localization and transmembrane transporter activity, as well as cilia or flagella dependent cell movement. In the enrichment analysis of KEGG pathway, the three comparison groups all enriched the largest number of differential genes in the branch pathway of KEGG metabolism, followed by the branch pathway of environmental information processing.

Conclusion: In F13-10 vs F13-5, the differential genes were mainly concentrated in 20 pathways such as ATP-binding cassette transport (ABC) transporters, thiamine metabolism and flagella assembly; In F13-25 vs F13-5, the differential genes are mainly concentrated in 20 pathways, such as (ABC) transporters, arginine and proline metabolism, two-component system and so on; In F13-25 vs F13-10, the differential genes are mainly concentrated in 20 pathways such as various types of glycan synthesis, two-component system and arginine metabolism.

Keywords: Low temperature bacteria; psychrophilic mechanism; transcriptome analysis.

Figure 1.

PCA plot of all samples.

Figure 2.

Sample correlation heat map. The branches represent clustering branches, and the color from blue to red indicates that the correlation gradually increases.

Figure 3.

Venn diagram of the number distribution of differentially expressed genes between groups. With $|$log2 (Fold Change)$|$$>$ 5 as the threshold, genes with $|$log2 (FoldChange)$|$$>$ 5 were defined as highly expressed genes.

Figure 4.

GO enrichment scatter plot of differentially expressed genes. A: The vertical axis represents the name of the GO term, and the name is sorted according to the Qvalue from small to large. The horizontal axis represents the enrichment factor. The larger the enrichment factor, the greater the degree of enrichment; the size of the point represents the number of differentially expressed genes in this GO term how much to count; The color of the point corresponds to different Qvalue values, ranging from 0 to 1, the closer to zero, the closer to the lighter color, the more significant the enrichment, and select the 20 GO terms with the most significant enrichment (if the enrichment If there are less than 20 terms, all will be displayed), and the GO enrichment scatter diagram of differentially expressed genes in Fig. 4 is drawn.

Figure 4.

Continued. B: The vertical axis is the name of the KEGG metabolic pathway, and the horizontal axis is the number of transcripts annotated to this pathway. The KEGG pathways involved in transcripts are divided into five branches: cellular processes, environmental information processing, genetic information processing, metabolism, and organic systems.

Figure 5.

KEGG enrichment scatter diagram of differentially expressed genes. Note: The vertical axis represents the name of each pathway, the order of Qvalue is from small to large, and the horizontal axis represents the enrichment factor. The larger the enrichment factor, the greater the degree of enrichment; The size of the points in the figure indicates the number of differentially expressed genes in this GO term; points with different colors have different Qvalue values, and the value range is between 0 and 1. The closer to 0, the more significant the enrichment.