To investigate the effect of ALA on ROS accumulation and cell damage in leaves, concentrations of superoxide anion and hydrogen peroxide and the degree of cell damage were examined by NBT, DAB and EB, respectively. Compared with CK plants, there was no significant change in the ROS accumulation and cell damage in group A plants. In contrast, plants in the group S exhibited darker staining indicating that the cellular ROS accumulation was significantly higher and cells were more severely damaged than in plants notstressed. The group SA stained darker than the unstressed plants but slightly lighter compared to the group S showing lower ROS accumulation and less cellular damage. This observation suggested that exogenous ALA could reduce the ROS accumulation and cell damage in salt-stressed P. wutunensis (Fig. 2).
In addition, the MDA content and relative electrical conductivity (REC) were significantly higher in the group S compared to plants without stress and tended to increase with increasing stress timespans, reaching a maximum at T8 (equivalent to 16 days of salt stress). The activities of SOD, POD and CAT showed an increasing and then decreasing trend with increasing treatment time, reaching a maximum at T4. The decrease in antioxidant enzyme activity at T8 was probably due to prolonged stress. The MDA content and the REC of plants in the group SA showed an increasing trend compared with those in the CK and A groups, but the increase was significantly lower than that in the group S. The activity of antioxidant enzymes in the group SA also tended to increase and then decrease with increasing treatment time, reaching a maximum at T4, but its activity was significantly higher than that of the salt-treated group. The plants in both the CK and A groups were not stressed and there was no significant difference (Fig. 3). These results indicated that exogenous ALA could significantly improve the salt tolerance of P. wutunensis, and T4 was the key turning point for exogenous ALA to alleviate salt stress in our study.
Transcriptome analysis of exogenous ALA-treated P. wutunensis under salt stress
To further understand the molecular mechanism of salt-tolerance improvement by exogenous ALA in P. wutunensis, transcriptome analysis was performed with leaves from the group SA. Since T4 was the critical turning point for salt-stress alleviation by exogenous ALA, the sampling time points were chosen at 0 (control), 1, 2 and 4 d after ALA treatment. RNAs were extracted from 12 leaf samples (4 treatments × 3 biological replicates) for transcriptome sequencing, respectively.
After removing the low-quality reads, a total of 80.06 Gb of clean reads were obtained (Table S1). The percentages of Q30 and GC were 93.06–93.86% and 44.04–44.42%, respectively, indicating the high quality of the transcriptome sequencing data. The clean read data was used for reassembly. 209,438 transcripts were generated by Trinity software, corresponding to 189,370 unigenes. The average transcript length was 1281 bp and the N50 was 1907 bp (Table S2). All assembled unigenes were compared, annotated and classified against the KEGG, NR, SwissProt, Trembl, KOG, GO and Pfam databases using the BLAST software (Table S3). In addition, 3927 (2270 up-regulations and 1657 down-regulations), 2402 (1217 up-regulations and 1185 down-regulations) and 3486 (1702 up-regulations and 1784 down-regulations) DEGs (|log2FoldChange| ≥ 1 and FDR < 0.05) were identified in pairs of T0 vs T1, T0 vs T2 and T0 vs T4 respectively (Fig. S1). It could be concluded that ALA induced significant changes in gene expression levels in P. wutunensis under the salt stress.
To further assess the biological function of ALA-induced DEGs under the salt stress, GO and KEGG enrichment analyses were performed on DEGs. The GO categories significantly enriched in DEGs in T0 vs T1 were "plant-type secondary cell wall biogenesis", "hemicellulose metabolic process" and "anion homeostasis". The significantly enriched GO categories in T0 vs T2 were "galactosidase activity", "photosystem" and "photosystem II ". The DEGs in T0 vs T4 were mainly enriched in "endoplasmic reticulum lumen", "galactosidase activity", " cell wall modification" and "protein N-linked glycosylation" GO categories (Fig. S2).
The top 20 KEGG enrichment pathways with the lowest Q values in the three comparisons were shown in Fig. 5. In T0 vs T1, DEGs were significantly enriched in the "Phenylpropanoid biosynthesis", "Flavonoid biosynthesis" and "Photosynthesis- antenna proteins" pathways. Similar to T0 vs T1, DEGs were also significantly enriched in the "Flavonoid biosynthesis" and "Photosynthesis - antenna proteins" pathways in T0 vs T2. Significant enrichment was also identified in the "Protein processing in endoplasmic reticulum" pathway. In T0 vs T4, DEGs were significantly enriched in the "plant hormone signal transduction", "protein processing in endoplasmic reticulum ", "N-Glycan biosynthesis", "protein export" and "phenylpropanoid biosynthesis", etc. These results indicated that ALA could exert effects on complex biological pathways of P. wutunensis under the salt stress (Fig. 4).
Effect of exogenous ALA on jasmonic acid signalling in P. wutunensis under salt stress
As plants adapt to external stresses by altering the expression of certain hormone levels which in turn will regulate gene expression, plant hormone signaling pathways need to be analyzed. The results showed that exogenous ALA mobilized several hormonal signals in plants, such as abscisic acid, jasmonic acid and growth hormone, with the jasmonic acid signaling pathway being significantly activated. In contrast to T0, exogenous ALA treatment under salt stress up-regulated the expression of several genes in the jasmonic acid biosynthetic pathway and the signal transduction pathway (Fig. 5A and B). The synthesis of JAs is essentially a cascade of enzymatic reactions starting with the release of linolenic acid from the cell membrane as a substrate. The expression levels of genes encoding JA synthesis-related proteins such as lipoxygenase (LOX2S), allene oxide cyclase (AOC), 12-oxophytodienoic acid reductase (OPR3) and acyl-CoA oxidase (ACX) were increased, especially in T0 vs T2 and T0 vs T4. Almost all genes in the JA signaling pathway were induced by ALA, with 8 (4 up-regulated and 4 down-regulated), 9 (all up-regulated) and 22 (20 up-regulated and 2 down-regulated) DEGs in T0 vs T1, T0 vs T2 and T0 vs T4 respectively. Under the ALA-treatment, in addition to jasmonic acid-amino synthetase (JAR1) and coronatine-insensitive protein 1 (COI1), which were significantly up-regulated, four MYC2, a core regulatory factor, were strongly induced by ALA to significantly higher expression levels. The expression levels of eight jasmonate ZIM domain-containing protein (JAZ) were also affected. These results indicated that the application of exogenous ALA positively regulated the accumulation of Jasmonates in P. wutunensis and activated the jasmonic acid signaling pathway, which was likely to be the key for ALA to improve salt-tolerance.
Jasmonic acid (JA) is an important hormone which regulates salt-tolerance in plants. Methyl jasmonate (MeJA) is a volatile ester form of JA that regulates the expression of genes associated with plant defense mechanisms in response to biotic and abiotic stresses. Therefore, a LC-MS/MS platform was used to assess whether the ALA-treatment affected the levels of MeJA in leaves of P. wutunensis under normal and salt-stressed conditions. Exogenous spraying of ALA under normal conditions had no significant effect on MeJA levels in P. wutunensis. However, the MeJA production was triggered by ALA with the salt treatment. Under salt stress, exogenous ALA significantly increased MeJA levels by 216% compared to the group S, indicating that MeJA accumulation might be induced by ALA (Fig. 5C).
To investigate the role of MeJA in ALA-induced salinity tolerance, seedlings were pretreated with 200 µM salicylhydroxamic acid (Jasmonates biosynthesis inhibitor, SHAM) and then analyzed for changes in the MDA content, the relative conductivity and antioxidant enzyme activities. The MDA content and REC were significantly higher in all plants under salt stress compared to CK, indicating that salt stress caused membrane lipid damages in the plants. Under salt stress, plants in the SA and SMJ groups showed significantly lower MDA content and REC compared to the group S, indicating that both MeJA and ALA alleviated the membrane lipid damage caused by salt stress. SHAM which should inhibit endogenous MeJA biosynthesis had no significant effect on the REC of plants in the group SS compared to the group S. On the other hand, plants in the group SSA underwent a significant increase in the MDA content compared to plants in the SA and SMJ groups, indicating that the ability of ALA to alleviate the membrane lipid damage was affected after inhibition of endogenous MeJA synthesis (Fig. 6A and B).
Salt stress significantly increased SOD, POD and CAT activities compared to CK. MeJA treatment increased SOD, POD and CAT activities compared to the group S, with a better effect at 200 µM, while SHAM-treatment significantly reduced the antioxidant enzyme activities. Under salt stress, the antioxidant enzyme activities of plants in the group SSA were significantly reduced compared to the group SA, indicating that the antioxidant capacity of ALA was affected by the inhibition of endogenous MeJA synthesis. These results suggested that the exogenous ALA-enhancement of salt-tolerance in P. wutunensis was mediated by the endogenous MeJA production. (Fig. 6C, D and E).
Effect of exogenous ALA on protein processing-related to the endoplasmic reticulum pathways of P. wutunensis under salt stress
According to the KEGG pathway analysis, ALA-treatment up-regulated the expression levels of a substantial number of genes in the protein processing in endoplasmic reticulum of P. wutunensis under thevsalt stress (Fig. 7A). There were 51 (33 up-regulated and 18 down-regulated), 54 (41 up-regulated and 13 down-regulated) and 160 (145 up-regulated and 15 down-regulated) DEGs in the protein processing in endoplasmic reticulum pathway in T0 vs T1, T0 vs T2 and T0 vs T4, respectively. These genes were annotated to encode enzymes which covered almost the entire spectrum of protein processing in endoplasmic reticulum, including mannosyl-oligosaccharide alpha-1,3-glucosidase (GlcII), calnexin (CNX), calreticulin (CRT), mannosyl-oligosaccharide alpha-1,2-mannosidase (ERMan I), GTP-binding protein (SAR1), UDP-glucose:glycoprotein glucosyltransferase (UGGT), oligosaccharyltransferase complex subunit (OSTs) and protein disulfide-isomerase (PDIs), as well as various molecular chaperones such as Heat shock protein 70 (Hsp70), Heat shock protein 90 (Hsp90), nucleotide exchange factors (NEFs), binding protein (BiP) and Glucose-related protein 94 (GRP94), all of which were up-regulated. At the same time, sub-pathways associated with endoplasmic reticulum processing such as N-glycan biosynthesis and protein export (Fig. 7B and C) were also significantly enriched in the similar pattern. In T0 vs T4 there were 30 (26 up-regulated and 4 down-regulated) and 19 (18 up-regulated and 1 down-regulated) DEGs enrichments in N-glycan biosynthesis and protein export, respectively. DEGs such as N-acetylglucosamine-1-phosphate transferase (ALG7) and dolichol kinase (DOLK) were significantly up-regulated in N-glycan biosynthesis. In the protein export pathway, DEGs such as protein transport protein (Sec61), signal peptidase (SEC11) and BiP were significantly up-regulated. The up-regulation of key genes in the N-glycan biosynthesis and protein export pathways could accelerate the transporting efficiency of unfolded nascent peptides to the endoplasmic reticulum via the Sec61 transport system, while providing sufficient N-glycans for protein glycosylation modifications. These results showed that ALA largely influenced the protein processing in endoplasmic reticulum pathway of P. wutunensis under salt stress by accelerating the folding efficiency of correctly folded proteins with helping proteins and directing the degradation of misfolded proteins.
Soluble proteins are important osmoregulatory molecules protecting the vital substances of cells and biofilms. Soluble proteins include enzymes that are involved in various metabolisms and also play important roles in the salt-resistance of plants. Additionally, the soluble protein content also reflects the efficiency of protein folding in the endoplasmic reticulum. In this study, the content of soluble proteins of plants in the group S was increased compared to the group CK. Both MeJA and ALA treatments significantly increased the soluble-protein content compared to the group S, while inhibition of MeJA synthesis with SHAM decreased it. Under salt stress, the soluble-protein content of plants in the group SSA was significantly lower than those in the SA / SMJ group, indicating that the ability of ALA to increase protein folding efficiency was hindered by the inhibition of endogenous MeJA synthesis (Fig. 7D).
Effect of exogenous ALA on the flavonoid biosynthesis pathway in P. wutunensis under salt stress
To investigate the effect of exogenous ALA on the flavonoid biosynthetic pathway of P. wutunensis under salt stress, relevant DEGs were screened and analyzed (Fig. 8A). In ALA-treated and salt-stressed plants, the expression levels of phenylalanine ammonia-lyase PAL, cinnamate 4-hydroxylase C4H and 4-Coumarate-CoA ligase 4CL (genes belonged to the early stages of the flavonoid synthesis pathway) were slightly reduced, but the transcription of chalcone synthase CHS (gene catalyzed the conversion of coumaroyl-CoA and malonyl-CoA together into chalcone) was significantly up-regulated by more than four times of the control. Dihydroflavonol 4-reductase (DFR) and Anthocyanin Synthase (ANS) are key enzymes in the flavonoid pathway for the synthesis of anthocyanins and proanthocyanidins. Four DFR and two ANS homolog genes were found to be upregulated in this study. In addition, the expression levels of other flavonoid biosynthesis-related genes including three CHS, five chalcone isomerase (CHI), one naringenin 3-dioxygenase (F3H) and one flavonoid-3'hydroxylase (F3'H) were also found increased. Flavonoid compounds such as flavonols, anthocyanins and proanthocyanidins are antioxidants and flavonoid compounds might act as important mediators of ALA, enhancing the scavenging of ROS and mitigating oxidative damage caused by salt stress.
Flavonoids, which possess oxygen-radical scavenging functions, participate in the integrated plant defense system to reduce cell damages from adverse stresses and thus to protect cells. In order to verify the relationship between ALA, MeJA and flavonoid compounds, the flavonoid content was examined under different treatments. Salt stress could increase the flavonoid content in treated plants compared to CK plants. Flavonoid content was significantly increased in plants treated with JA and especially with ALA compared to the group S. Compared to the group SS, the ALA-treatment with JA-biosynthesis inhibition still increased the flavonoid content to a similar level as in the only ALA-treated plants. This observation suggested that ALA would increase the flavonoid content through inducing the accumulation of MeJA in P. wutunensis but there might well be other ALA-induced signaling pathways existed besides the MeJA pathway to perceive and resist salt stress (Fig. 8B).
Quantitative RT-PCR validation
To test the accuracy of our RNA-Seq data, quantitative RT-PCR (qRT-PCR) was performed on 11 DEGs included MYC2, JAR1, JAZ, AOC, LOX2S, OPR, BIP, Doa10, CHI, DFR and PAL, which were selected from the jasmonic acid biosynthetic and the signal transduction pathway, protein processing in endoplasmic reticulum pathway and flavonoids biosynthesis pathway. Consistently, the qRT-PCR results exhibited the same trend which were correlated with the RNA-Seq data (R2 = 0.81674), thus confirming the confidentiality of the RNA-Seq data (Fig. 9).