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. 2015 Aug;22(4):245-57.
doi: 10.1093/dnares/dsv012. Epub 2015 Jul 23.

A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues

Xue-mei Zhou  1 , Peng Zhao  1 , Wei Wang  1 , Jie Zou  2 , Tian-he Cheng  1 , Xiong-bo Peng  1 , Meng-xiang Sun  3
Affiliations

A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues

Xue-mei Zhou et al. DNA Res. 2015 Aug.

Abstract

Autophagy is an evolutionarily conserved mechanism in both animals and plants, which has been shown to be involved in various essential developmental processes in plants. Nicotiana tabacum is considered to be an ideal model plant and has been widely used for the study of the roles of autophagy in the processes of plant development and in the response to various stresses. However, only a few autophagy-related genes (ATGs) have been identified in tobacco up to now. Here, we identified 30 ATGs belonging to 16 different groups in tobacco through a genome-wide survey. Comprehensive expression profile analysis reveals an abroad expression pattern of these ATGs, which could be detected in all tissues tested under normal growth conditions. Our series tests further reveal that majority of ATGs are sensitive and responsive to different stresses including nutrient starvation, plant hormones, heavy metal and other abiotic stresses, suggesting a central role of autophagy, likely as an effector, in plant response to various environmental cues. This work offers a detailed survey of all ATGs in tobacco and also suggests manifold functions of autophagy in both normal plant growth and plant response to environmental stresses.

Keywords: autophagy; environmental stresses; gene expression; signalling; tobacco.

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Figures

Figure 1.
Figure 1.
Phylogenetic relationship of ATGs from N. tabacum and A. thaliana. The tree was calculated with MEGA 5.1 software using the maximum parsimony method.
Figure 2.
Figure 2.
The structure divergence of ATG1s and ATG18s. This figure is available in black and white in print and in colour at DNA Research online.
Figure 3.
Figure 3.
RT-PCR examination of the transcripts of ATGs in N. tabacum. The cDNA prepared from root, stem, leaf, pollen, anther, seeds (4, 8 and 14 days after pollination, respectively) were selected as templates for PCR. GAPDH was used as the control.
Figure 4.
Figure 4.
Expression profile of NtATGs in different tissues under normal conditions of plant growth. Expression profile of NtATGs in tobacco, which is constructed based on the relative expression level of each ATGs in different tissues. The expression level was normalized to GAPDH (AJ133422), Polyubiquitin (GQ281244), Actin (GQ281246) and Elongation factor 1a (AF120093). Blue box indicates the lower transcriptional level of ATGs, whereas red box indicates the higher expression level of ATGs. Scale bar represents fold change (log2 value).
Figure 5.
Figure 5.
Dynamic changes in NtATGs during the process of seed development. Expression profile of NtATGs in tobacco, which is constructed based on the relative expression level of each ATG in seeds at different developmental stages. The expression level was normalized to GAPDH (AJ133422), Polyubiquitin (GQ281244), Actin (GQ281246) and Elongation factor 1a (AF120093). Data represent relative expression level (log2 value). This figure is available in black and white in print and in colour at DNA Research online.
Figure 6.
Figure 6.
Expression profile of NtATGs in seedlings under sucrose and nitrogen starvation. Relative expression levels of each ATG in seedlings under sucrose and nitrogen starvation were normalized to GAPDH (AJ133422), Polyubiquitin (GQ281244), Actin (GQ281246) and Elongation factor 1a (AF120093). The expression level of each ATG was calculated and compared with that in seedlings under normal growth conditions. The expression level of each ATG in seedlings under normal growth conditions was indicated with grey box (0). Blue box indicates the lower transcriptional level of ATGs, whereas red box indicates the higher expression level of ATGs. Scale bar represents fold change (log2 value).
Figure 7.
Figure 7.
Expression profile of NtATGs in seedlings under dark, cold, drought and salt stresses. Relative expression levels of each ATG in seedlings under dark, cold, drought and salt stresses were normalized to GAPDH (AJ133422), Polyubiquitin (GQ281244), Actin (GQ281246) and Elongation factor 1a (AF120093). The expression level of each ATG was calculated and compared with that in seedlings under normal growth conditions. The expression level of each ATG in seedlings under normal growth conditions was indicated with grey box (0). Blue box indicates the lower transcriptional level of ATGs, whereas red box indicates the higher expression level of ATGs. Scale bar represents fold change (log2 value).
Figure 8.
Figure 8.
Expression profile of NtATGs in seedlings under heavy metal stresses. Relative expression levels of each ATG in seedlings under heavy metal stresses were normalized to GAPDH (AJ133422), Polyubiquitin (GQ281244), Actin (GQ281246) and Elongation factor 1a (AF120093). The expression level of each ATG was calculated and compared with that in seedlings under normal growth conditions. The expression level of each ATG in seedlings under normal growth conditions was indicated with grey box (0). Blue box indicates the lower transcriptional level of ATGs, whereas red box indicates the higher expression level of ATGs. Scale bar represents fold change (log2 value).
Figure 9.
Figure 9.
Expression profile of NtATGs in seedlings under different hormone treatments. Relative expression levels of each ATG in seedlings under different hormone treatments were normalized to GAPDH (AJ133422), Polyubiquitin (GQ281244), Actin (GQ281246) and Elongation factor 1a (AF120093). The expression level of each ATG was calculated and compared with that in seedlings under normal growth conditions. The expression level of each ATG in seedlings under normal growth conditions was indicated with grey box (0). Blue box indicates the lower transcriptional level of ATGs, whereas red box indicates the higher expression level of ATGs. Scale bar represents fold change (log2 value).
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