C-terminally encoded peptides (CEPs) are potential mediators of abiotic stress response in plants

Abstract

Intracellular signaling is a critical determinant of the normal growth and development of plants. Signaling peptides, also known as peptide hormones, along with classical phytohormones, are the significant players of plant intracellular signaling. C-terminally encoded peptide (CEP), a 15-amino acid post-translationally peptide identified in Arabidopsis, plays a pivotal role in lateral root formation, nodulation, and act as long-distance root to shoot signaling molecule in N-starvation conditions. Expression of CEP gene members in Arabidopsis is perturbed by nitrogen starvation; however, not much is known regarding their role in other abiotic stress conditions. To gain a comprehensive insight into CEP biology, we identified CEP genes across diverse plant genera (Glycine max, Sorghum bicolor, Brassica rapa, Zea mays, and Oryza sativa) using bioinformatics tools. In silico promoter analysis revealed that CEP gene promoters show an abundance of abiotic stress-responsive elements suggesting a possible role of CEPs in abiotic stress signaling. Spatial and temporal expression patterns of CEP via RNA seq and microarray revealed that various CEP genes are transcriptionally regulated in response to abiotic stresses. Validation of rice CEP genes expression by qRT-PCR showed that OsCEP1, OsCEP8, OsCEP9, and OsCEP10 were highly upregulated in response to different abiotic stress conditions. Our findings suggest these CEP genes might be important mediators of the abiotic stress response and warrant further overexpression/knockout studies to delineate their precise role in abiotic stress response.

Keywords: Abiotic stress; C-terminally encoded peptide (CEP); Signaling peptides; qRT-PCR.

Fig. 1

Chromosomal localization of the CEP gene in different plant genera. Chromosomal distribution of CEP genes in a rice, b Sorghum bicolor, c Glycine max, d Brassica rapa, e Zea mays. The chromosomal position, along with the CEP gene name, is marked on the chromosome. The only chromosome with CEP genes is shown. Tandemly duplicated gene pairs are highlighted in red (color figure online)

Fig. 2

Heatmap representing the presence or absence of cis-acting regulatory elements (CAREs) in all the identified CEP genes. The CAREs are divided into broad categories based on their function. These categories are depicted on top of the heatmap

Fig. 3

Plot showing an abundance of probable transcription factors that might bind to the promoter of CEP genes. Word plot showing an abundance of transcription factors that might bind in the upstream region of CEP genes across different genera. Transcription factor enrichment was done using PlantRegMap. Word size is directly proportional to the number of times any transcription factor was reported as enriched with a p-value cutoff of 0.05

Fig. 4

Heatmap depicting expression level of CEP genes at different developmental stages across various plant genera. The expression of CEP genes at different stages of development in a rice, b Sorghum bicolor, c Brassica rapa, d Zea mays, and e Glycine max. FPKM values were scaled and centered before creating the heatmap

Fig. 5

Expression level of CEP genes under different abiotic stress conditions based on publicly available a microarray and b RNA seq data. Heatmap analysis of expression of CEP genes a(i) in 7-day old IR64 seedlings under different abiotic stress conditions such as salinity, drought, and cold stress. a(ii) in 7-day old IR64 seedlings incubated for 3 h in different hormone solutions such as abscisic acid (AbA), salicylic acid (SA), jasmonic acid (JA) and 1-aminocyclopropane-1carboxyclic acid (ACC). a(iii) in 10-day old IR64 seedlings grown in Hewit solution and treated with 100 µm of chromium (Cr), Cadmium (Cd), Arsenic (As), and Lead (Pb). The green color represents down-regulation of the gene; black color represents no change in expression level, while red color represents up-regulation with respect to control samples. Heatmap representing log2 fold change of various CEP genes in different plants in different abiotic stress conditions based on RNA seq data b(i) from Nipponbare in salinity stress b(ii) cold stress and b(iii) cadmium stress. b(iv) Heatmap showing expression of CEP genes in Glycine max under salinity and drought stress at different time points. b(v) Heatmap representing the expression of CEP genes in response to cold and heat stress in different Zea mays varieties (Mo17, Oh43, B70). b(vi) Heatmap representing the expression of CEP genes in Zea mays varieties (Mo17, Oh43, B70) under drought stress. b(vii) Heatmap representing the expression of CEP genes from Sorghum bicolor shoot and root tissues under ABA and PEG

Fig. 6. Expression profile of CEP genes in response to different abiotic stress conditions

The expression level of CEP genes in rice variety IR64 in response to various abiotic stress conditions [drought and salinity (200 mM)] for 1 h and 24 h duration in a shoots and b roots were obtained by qRT-PCR. The expression level of CEP genes in control samples without any stress was set as 1, and the fold change values were plotted in the form of a bar graph. All qRT-PCR experiments were done with three biological replicates and three technical replicates. The standard deviation of three biological replicates has been shown by error bars