Comparative transcriptome analysis reveals significant differences in the regulation of gene expression between hydrogen cyanide- and ethylene-treated Arabidopsis thaliana

Abstract

Background: Hydrogen cyanide (HCN) is a small gaseous molecule that is predominantly produced as an equimolar co-product of ethylene (ET) biosynthesis in plants. The function of ET is of great concern and is well studied; however, the function of HCN is largely unknown. Similar to ET, HCN is a simple and diffusible molecule that has been shown to play a regulatory role in the control of some metabolic processes in plants. Nevertheless, it is still controversial whether HCN should be regarded as a signalling molecule, and the cross-talk between HCN and ET in gene expression regulation remains unclear. In this study, RNA sequencing (RNA-seq) was performed to compare the differentially expressed genes (DEGs) between HCN and ET in Arabidopsis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were subsequently performed to investigate the function and pathway enrichment of DEGs. Parts of key genes were confirmed by quantitative real-time PCR.

Results: The results showed that at least 1305 genes and 918 genes were significantly induced by HCN and ET, respectively. Interestingly, a total of 474 genes (|log₂ FC| ≥1) were co-regulated by HCN and ET. GO and KEGG analyses indicated that the co-regulated genes by HCN and ET were enriched in plant responses to stress and plant hormone signal transduction pathways, indicating that HCN may cooperate with ET and participate in plant growth and development and stress responses. However, a total of 831 genes were significantly induced by HCN but not by ET, indicating that in addition to ET, HCN is in essence a key signalling molecule in plants. Importantly, our data showed that the possible regulatory role of a relatively low concentration of HCN does not depend on ET feedback induction, although there are some common downstream components were observed.

Conclusion: Our findings provide a valuable resource for further exploration and understanding of the molecular regulatory mechanisms of HCN in plants and provide novel insight into HCN cross-talk with ET and other hormones in the regulation of plant growth and plant responses to environmental stresses.

Keywords: Arabidopsis thaliana; Ethylene; Hydrogen cyanide; RNA-seq.

Fig. 1

The number of Unigenes analyzed in this experiments

Fig. 2

Comparison of DEGs number between CK vs HCN and CK vs ET. a Comparison of all DEGs regulated by HCN and ET. b The number of DEGs (fold change ≥2) regulated by HCN and ET was compared

Fig. 3

Venn diagram of DEGs regulated by HCN and ET. a Venn diagram of all DEGs from CK vs HCN and CK vs ET. b Venn diagram of DEGs (fold change ≥2) from CK vs HCN and CK vs ET

Fig. 4

DEGs were exclusively-regulated by HCN or ET, respectively. a Heatmap of significantly regulated DEGs (fold change ≥2) by HCN. b Heatmap of significantly regulated DEGs (fold change ≥2) by ET. c The number of DEGs specific-regulated by HCN or ET, respectively

Fig. 5

Comparison of GO terms enriched in CK vs HCN and CK vs ET. a-c Comparison of the numbers of GO terms between CK vs HCN and CK vs ET based on the P-values (P < 0.05) and false discovery rate (FDR < 0.05). d and e The GO categories of biological process, cellular component and molecular function were compared between CK vs HCN and CK vs ET based on the P < 0.05 and FDR < 0.05, respectively

Fig. 6

Comparison of top 30 GO terms between CK vs HCN and CK vs ET. The DEGs were assigned to biological process (BP) were analyzed and compared between them

Fig. 7

Comparison of KEGG pathways enriched in CK vs HCN and CK vs ET. a Comparison of KEGG terms (P < 0.05) between CK vs HCN and CK vs ET. b The KEGG pathways enriched in CK vs HCN. c The common KEGG pathways enriched in CK vs HCN and CK vs ET. (d) The KEGG pathways enriched in CK vs ET

Fig. 8

The DEGs involved in ethylene biosynthetic process and ethylene-activated signaling pathways from CK vs HCN. a The DEGs of CK vs HCN involved in ethylene biosynthetic process. b The DEGs of CK vs HCN involved in ethylene-activated signaling pathway

Fig. 9

Comparison of stress-related genes that were regulated by HCN and ET. a Response to stress. b Response to abiotic stress. c Response to biotic stress. d Response to salt stress. e Response to osmotic stress. f Response to oxidative stress. The DEGs of fold change ≥2 were compared and analyzed