Content uploaded by Biao Gong
Author content
All content in this area was uploaded by Biao Gong on Oct 20, 2022
Content may be subject to copyright.
Using Transcriptome to Discover a Novel Melatonin-Induced
Sodic Alkaline Stress Resistant Pathway in
Solanum lycopersicum L.
Yanyan Yan
1,2,3,4
, Xin Jing
1,2,3,4
, Huimeng Tang
1,2,3,4
, Xiaotong Li
1,2,3,4
, Biao Gong
1,2,3,4,
* and
Qinghua Shi
1,2,3,4,
*
1
State Key Laboratory of Crop Biology, Tai’an, P.R. China
2
Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, P.R. China
3
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, P.R. China
4
College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, P.R. China
*Corresponding authors: Biao Gong, E-mail, gongbiao@sdau.edu.cn; Fax, +86 538 8249907; Qinghua Shi, E-mail, qhshi@sdau.edu.cn;
Fax, +86 538 8242201.
(Received March 17, 2019; Accepted June 20, 2019)
Melatonin plays important roles in multiple stress responses.
However, the downstream signaling pathway and molecular
mechanism are unclear until now. Here, we not only re-
vealed the transcriptional control of melatonin-induced
sodic alkaline stress tolerance, but also described a screen
for key downstream transcriptional factors of melatonin
through transcriptome analysis. The melatonin-induced
transcriptional network of hormone, transcriptional factors
and functional genes has been established under both con-
trol and stress conditions. Among these, six candidates of
transcriptional factors have been identified via Gene
Ontology and Kyoto Encyclopedia of Genes and Genomes
analysis. Using the virus-induced gene silencing approach,
we confirmed that DREB1and IAA3 were key downstream
transcriptional factors of melatonin-induced sodic alkaline
stress tolerance at the genetic level. The transcriptions of
DREB1and IAA3 could be activated by melatonin or sodic
alkaline treatment. Interestingly, we found that DREB1a
could directly upregulate the expression of IAA3 by binding
to its promoters. Moreover, several physiological processes
of Na
+
detoxification, dehydration resistance, high pH buf-
fering and reactive oxygen species scavenging were con-
firmed to depend or partly depend on DREB1and IAA3
pathway in melatonin-induced stress tolerance. Taken to-
gether, this study suggested that DREB1and IAA3 are posi-
tive resistant modulators, and provided a direct link among
melatonin, DREB1and IAA3 in the sodic alkaline stress
tolerance activating in tomato plants.
Keywords: DREB1IAA3 Melatonin Sodic alkaline
stress Tomato Transcriptome.
Introduction
As an extreme reflection of desertification, salinity–alkalinity
has an augmented impact on the growth and productivity of
crops in arid and semiarid regions (Pang et al. 2016). Saline soil
is mainly due to the accumulation of NaCl, NaNO
3
and
Na
2
SO
4
. Excepting these neutral salts, there are much of
NaHCO
3
and Na
2
CO
3
in sodic alkaline soil (Gong et al.
2013). As a result, plants growing in sodic alkaline soil also
suffer due to Na
+
, high pH and osmotic stress, which has
been demonstrated to cause more serious damage to plants
when compared with saline stress (Gong et al. 2015).
Unfortunately, more than half of the saline-alkaline soil is
sodic alkaline salts throughout the world (FAO; http://www.
fao.org/home/en/). So, with the increasing recognition of the
threat posed by sodic alkaline stress to agricultural production,
literature about plant response and adaption to sodic alkaline
stress has been flourished in recent years (Gong et al. 2014a,
Gong et al. 2014b, Gong et al. 2015).
Melatonin (N-acetyl-5-methoxytryptamine) has been recog-
nized as an important neurohormone for mammals in the last
decades. Since the first discovery of melatonin in several edible
plants in 1995 (Dubbels et al. 1995), many pharmacological studies
have been performed to investigate its functional and physio-
logical significance. In recent years, large numbers of literature
emerged about potential roles of melatonin as growth factor or
defense responses biostimulator in a series of plants by enhancing
their seed germination, seedling growth, root development, nutri-
ent absorption, flowering, fruit ripening, as well as abiotic and
biotic stress tolerances, including extreme temperature, drought,
salinity–alkalinity, heavy metals, oxidative stress, as well as patho-
gen infection and insect herbivory (Fan et al. 2018, Y. Wang et al.
2018, Xu et al. 2018). Until now, nearly all studies indicated that
melatonin, as either a stress-induced agent or a protective mol-
ecule, plays a critical role in reactive oxygen species (ROS) scaven-
ging to improve a wide spectrum of stress tolerance in plants
(Martinez et al. 2018). Credible evidence suggests that melatonin
should be classified as a mitochondria-targeted antioxidant (Tan
and Reiter 2019); melatonin achieves its antioxidant capacity via
direct detoxification of ROS and reactive nitrogen species and
indirectly by stimulating antioxidant enzymes while suppressing
the activity of pro-oxidant enzymes (Zhang and Zhang 2014,
Wang et al. 2017). Naturally, the exogenous application of mela-
tonin has been considered to elevate antioxidant levels against
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126, Advance Access publication on 3 July 2019,
available online at https://academic.oup.com/pcp
!The Author(s) 2019. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.
For permissions, please email: journals.permissions@oup.com
Regular Paper
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
stress conditions, which is a generally physiological mechanism to
reveal melatonin-induced stress tolerance in organisms (Debnath
et al. 2018). Recently, rapidly increasing evidences show that mela-
tonin, acting as a phytohormone-like molecule or secondary mes-
senger, implicated in many signaling events, including stress
response in plants. In mammals, numerous regulatory actions of
melatonin are mediated by melatonin receptor type 1 or type 2
(Bonnefond et al. 2012). More recently, CAND2/PMTR1 has been
identified as melatonin receptor in Arabidopsis (Wei et al. 2018).
So, the roles of melatonin in stress response need to be widely
investigated in terms of the signaling pathway.
The understanding on the signaling transduction and molecu-
lar mechanisms of melatonin-induced stress tolerance in plants
has been focused by scientists. At the molecular level, the percep-
tion of extracellular stimuli and subsequent activation of appro-
priate responses require a complex interplay of signaling cascades,
in which phytohormones and transcriptional factors play the crit-
ical roles. It has been shown that phytohormones cooperate with
transcriptional factors to regulate the protective processes of
plants against stressors through synergistic and antagonistic
cross talk (Long and Benfey 2006). Using this kind of cross talk,
transcriptional factors directly accept commands from upstream
phytohormones, and then regulate the transcription of down-
stream stress-responsive genes or act in cross talk among multiple
signaling pathways. Until now, several important stress-responsive
transcriptional factors have been confirmed in melatonin-
mediated signaling in Arabidopsis thaliana.Insummary,thecyst-
eine 2/histidine 2-type transcription factor zinc finger protein 6
(ZAT6)-activated C-receptor-binding factor (CBF)pathwayis
required for melatonin-induced freezing stress tolerance (Shi and
Chan 2014). CBF signaling and sugar accumulation have been re-
ported partly to involve in melatonin-induced wide spectrum of
stress tolerance (Shi et al. 2015b). Additionally, the diurnal changes
of CBF transcriptional level maybe influenced by the correspond-
ing change of melatonin level and be involved in the diurnal cycle
of plant immunity (Shi et al. 2016). As the master regulator of the
heat stress response, the transcription of class A1 heat-shock fac-
tors (HSFA1s) can be activated by exogenous melatonin, which
induces transcripts of a series of heat-responsive genes to improve
the thermotolerance (Shi et al. 2015d). Moreover, a thermotoler-
ance-related heat-shock protein 90s (HSP90s) is also required for
melatonin-induced resistance to Fusarium wilt in Musa acuminate
(Wei et al. 2017). For auxin signaling pathway, indole-3-acetic acid
inducible 17 (IAA17) has been identified to positively modulate
natural leaf senescence through melatonin-mediated pathway (Shi
et al. 2015c). Excepting melatonin-induced downstream transcrip-
tional factors, HSFA1s was also highlighted to act as an upstream
regulator to increase melatonin biosynthesis to confer cadmium
tolerance in tomato plants (Cai et al. 2017). Thus, these transcrip-
tional factors may constitute a global and complicated signaling
network of melatonin-mediated stress responses in plants. Though
some transcriptional factors have been identified to involve in
melatonin signaling in A. thaliana; to data, it is largely unknown
which transcriptional factors are involved in melatonin-induced
sodic alkaline stress tolerance, especially in crop species.
Tomato is one of the world’s largest vegetable crops, with an
annual production of 177 million metric tons in 2017, among
which >31% were produced in China (FAO; http://www.fao.
org/home/en/). Large numbers of studies showed that low crop
yields were usually obtained under saline–alkaline conditions;
however, for tomato crops, moderate salinity–alkalinity can
enhance the fruit quality and nutritional components (Saito
and Matsukura 2015). In the current Chinese market, such
fruits are referred to as ‘fruit tomatoes’ and are sold at a
higher price compared with normally cultivated tomatoes be-
cause of their high sugar content and excellent flavor. Thus,
using chemical or genetic approach to improve tomato sodic
alkaline stress tolerance seems to be significant for the utiliza-
tion of saline–alkaline soil and high-quality tomato production.
We have previously reported that exogenous application of
0.5 mM melatonin can enhance sodic alkaline stress tolerance by
improving ROS metabolism and ion homeostasis in tomato
plants (Liu et al. 2015b). Subsequently, we have observed un-
expectedly that melatonin also triggers a periodic increase in
nitric oxide level, which functions as a signaling molecule in
increasing sodic alkaline stress response (Liu et al. 2015a) and
adventitious root formation (Wen et al. 2016) in tomato plants.
In this study, we want to combine transcriptome data with
genetic verification to unravel the signaling events of mela-
tonin-induced sodic alkaline stress tolerance at both omics
level and molecular level in tomato plants. The results can
provide wide and detailed evidence for the reference of chem-
ical and genetic approaches in improving melatonin-induced
sodic alkaline stress tolerance in tomato plants.
Results
Melatonin induces sodic alkaline stress tolerance
After 10 d of sodic alkaline treatment, the growth of shoot and
root, water contents, photosynthetic parameters and chloro-
phyll contents were significantly inhibited; at the same time,
the electrolyte leakage of roots and malondialdehyde (MDA)
content of leaves was significantly increased (Table 1;Fig. 1A).
However, exogenous application of melatonin to sodic alkaline-
stressed seedlings significantly improved these stress-related
parameters, but had little or no effect on nonstressed seedlings
(Table 1;Fig. 1A). It is important to note that treatment with
exogenous melatonin significantly enhanced the endogenous
melatonin level in both control and stress conditions, which
indicated that exogenous melatonin can be absorbed from the
environment, or the biosynthesis of melatonin can be induced
by its exogenous stimulus (Fig. 1B). Moreover, the level of en-
dogenous melatonin was significantly elevated in response to
sodic alkaline stress from 3 to 6 d but subsequently decreased.
These results indicated that melatonin is involved in the re-
sponse to sodic alkaline stress, but the response process is not
notably rapid and strong.
Quantitative identifications of differently
expressed genes by transcriptome sequencing
To investigate the mechanism underlying melatonin-induced
sodic alkaline stress tolerance in tomato plants, dynamic profil-
ing of the mRNA expression affected by melatonin and sodic
2052
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
alkaline treatments was performed via transcriptome sequen-
cing. Totally, 109 (42 upregulated genes and 67 downregulated
genes), 4,744 (1,765 upregulated genes and 2,979 downregu-
lated genes), 1,300 (595 upregulated genes and 705 downregu-
lated genes) and 1,891 (1,225 upregulated genes and 666
downregulated genes) differently expressed genes (DEGs)
were separately identified in contrastive groups of ‘C vs. M’,
‘C vs. S’, ‘C vs. SM’ and ‘S vs. SM’ (Fig. 1C; Supplementary
Table S3). It is important to note that the most numbers of
DEGs were shown in ‘C vs. S’; however, significantly reduced
numbers of DEGs were shown in ‘C vs. SM’ (Fig. 1C). This result
indicated that melatonin played important roles in restoring
the stress-disturbed gene expression in tomato roots. Venn
diagram analysis showed that 64 DEGs were influenced by
melatonin under both control and sodic alkaline stress condi-
tions (the intersection of ‘C vs. M’ and ‘S vs. SM’); additionally,
64 DEGs were influenced by only melatonin and sodic alkaline
stress (the intersection of ‘C vs. M’ and ‘C vs. S’); furthermore, 39
DEGs were identified in the intersection of ‘C vs. M’, ‘C vs. S’ and
‘S vs. SM’ (Fig. 1D), which implied that these genes responding
to both melatonin and sodic alkaline stress might be involved in
melatonin-induced sodic alkaline stress tolerance.
Functional classification by Gene Ontology
analysis
For insight into the functional categories, we used Gene
Ontology database to categorize the identified DEGs. The
Fig. 1 (A) Representative phenotypes of sodic alkaline stress mitigation by exogenous melatonin in tomato seedlings 10 d after treatment. (B) The
endogenous melatonin contents of tomato roots at the 0, 1, 3, 6 and 10 d after treatment. Data represent the means of five replicates (±SE). (C) Numbers
of DEGs in the transcriptome data of tomato roots 3 d after treatment. The detailed information of related DEGs can be observed in Supplementary Table
S3. Data represent the means of two replicates. (D) Venn diagram showing numbers of overlapping DEGs in the transcriptome data.
Table 1 Sodic alkaline stress mitigation of melatonin on tomato seedlings
PH SDW RDW Chl P
N
Fv/Fm EL MDA WC
C 39.5 ±3.1a 4.9 ±0.3a 0.59 ±0.05b 18.3 ±1.7a 18.2 ±1.9a 0.83 ±0.02a 21.2 ±1.6c 55.1 ±7.2c 91.7 ±1.3a
M 41.1 ±2.9a 5.2 ±0.3a 0.77 ±0.06a 17.9 ±1.9a 19.3 ±2.1a 0.82 ±0.02a 20.5 ±1.4c 51.2 ±8.1c 90.3 ±2.1a
S 21.6 ±3.1c 2.2 ±0.4c 0.25 ±0.07d 9.5 ±2.1c 8.9 ±3.6c 0.63 ±0.06c 55.3 ±3.7a 151.1 ±10.5a 79.5 ±3.3c
SM 30.5 ±3.8b 3.5 ±0.3b 0.38 ±0.05c 14.4 ±2.5b 14.1 ±3.1b 0.74 ±0.05b 34.8 ±4.1b 102.9 ±8.6b 85.8 ±3.7b
PH, plant height (cm); SDW, shoot dry weight (gplant
1
); RDW, root dry weight (gplant
1
); Chl, chlorophyll content (mg
1
gDW); P
N
, net photosynthetic rate
(mmolm
2
s
1
); F
v
/F
m
, the maximum PSII quantum yield; EL, electrolyte leakage of roots (%); MDA, malondialdehyde content of leaves (nmolg
1
DW); WC, water
content of leaves (%). All data were measured 10 d after treatment. Data represent the means of five replicates (±SE), and different letters are significantly different
(P<0.05).
2053
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
identified DEGs cover a wide range of cellular components,
molecular functions and biological processes and can be clas-
sified into 16, 17 and 20 categories, respectively (Supplementary
Fig. S1). The cellular component functions of these DEGs were
mainly related to the cell part, cell, organelle, membrane and
organelle part. The molecular functions of these DEGs were
mainly binding, catalytic activity, transporter activity, nucleic
acid binding transcription factor activity and structural mol-
ecule activity. The largest group within the biological process
category composed cellular process, followed by metabolic pro-
cess, single-organism process, response to stimulus and biolo-
gical regulation.
Functional classifications using Kyoto
Encyclopedia of Genes and Genomes pathways
Previous studies indicated that processes of metabolism and
energy conversion, and hormone signaling are sensitive to sodic
alkaline stress (Gong et al. 2014e). We then examined if mela-
tonin takes part in these processes to influence sodic alkaline
stress tolerance in tomato by referencing canonical pathways in
the Kyoto Encyclopedia of Genes and Genomes (KEGG; http://
www.genome.ad.jp/kegg/). Similar to previous studies, both
hormone signaling and metabolism and energy conversion
pathway were significantly enriched in the contrastive groups
of ‘C vs. S’ (Fig. 2; Supplementary Table S4). For hormone sig-
naling, a significant enrichment of auxin, abscisic acid, ethylene,
salicylic acid, jasmonic acid was shown in ‘C vs. S’. Excepting
auxin, the other four kinds of hormone are all stress- or senes-
cence-related hormone, which indicated that a senescent pro-
cess at hormone metabolism level was induced by sodic alkaline
stress. It is important to note that the enrichment of hormone
signaling pathways was completely abolished by applying mela-
tonin in ‘C vs. SM’. As we know, transcriptional factors usually
play a critical role in transmitting instruction from hormone
signaling to specific biological process including metabolism
and energy conversion. A significant enrichment of DEGs in
transcription factor pathway was shown in ‘C vs. M’ and ‘S vs.
SM’, which indicating that melatonin was took part in tran-
scriptional activation under both control and stress conditions.
In Fig. 2, little effects of melatonin has been shown in reg-
ulating metabolism and energy conversion (C vs. M); however,
sodic alkaline stress nearly influenced all metabolic processes,
such as the metabolism of starch, sucrose, fatty acid and nitro-
gen, as well as energy conversion including respiration and oxi-
dative phosphorylation (C vs. S). Importantly, the enrichment
of DEGs in ‘C vs. SM’ was significantly lower than ‘C vs. S’, which
provided a strong evidence that melatonin played important
roles in repairing sodic alkaline stress-induced abnormal expres-
sion of mRNA in metabolism and energy conversion.
The prediction of key genes involved in
melatonin-induced sodic alkaline stress tolerance
Given that a large group of genes altered by melatonin are
involved in plant stress tolerance, we further categorized
these genes according to their specific roles in melatonin-
induced sodic alkaline stress tolerance. A schematic of mela-
tonin-induced key events, including perception, signal trans-
duction, hormone signaling, transcriptional factors, response
to stress, as well as plant growth and development, were de-
picted in Fig. 3 and Supplementary Table S5. During the stress
response, stress perception involves one receptor which may
initiate a signal transduction cascade involving 24 DEGs. In
addition, 61 DEGs of hormone signaling were also examined
and included in the schematic, which played a critical role in
signaling during stress events by cross talk with 12 transcrip-
tional factors. Thus, a large quantity of DEGs involving in re-
sponse to stress, abiotic stress, oxidative stress, salt stress and
osmotic stress could be regulated by melatonin, which is benefit
for plant growth and development in stress conditions.
According to this schematic (Fig. 3), we noticed that pro-
cesses of transcriptional factors were shown in the central place,
which received signal and then regulated the downstream
genes’ transcription to influence the process of growth, devel-
opment and stress tolerance. With the purpose of discovering
the key regulatory genes of melatonin-induced sodic alkaline
stress tolerance, we also searched the DEGs of transcriptional
factors in ‘S vs. SM’. As a result, 156 DEGs of transcriptional
factors have been identified in ‘S vs. SM’. In order to reduce the
Fig. 2 Heat map analysis of key DEGs responding to melatonin and sodic alkaline stress in the transcriptome data. The detailed information of
related DEGs can be observed in Supplementary Table S4.
2054
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
range of key regulatory genes, we only selected the DEGs of
transcriptional factors with similar expressed patterns in both
‘C vs. M’ and ‘S vs. SM’. Fortunately, only six transcriptional
factors with similar expressively patterns by the quantitative
RT-PCR (qRT-PCR) analysis were eligible and shown in
Table 2. Thus, a genetic verification can be performed in the
following experiments.
DREB1aand IAA3 are key transcriptional factors
in melatonin-induced sodic alkaline stress
tolerance
In order to determine the roles of the six transcriptional factors
in melatonin-induced sodic alkaline stress tolerance in tomato
plants, HBP-1b,bHLH93,DREB1,IAA3,ZFP20 and GATA-5
were, respectively, silenced via virus-induced gene silencing
(VIGS) approach. Transcript analysis of the leaves revealed
that the transcripts of these six silenced plants were reduced
to 67–95% of the concentrations in empty TRV vector (pTRV)
control plants (Supplementary Table S6). Therefore, the tran-
scripts of all six transcriptional factors were substantially sup-
pressed in these VIGS plants.
We then determined whether suppressing the transcripts of
these genes had the ability to abolish melatonin-induced sodic
alkaline stress tolerance. Similar with wild type (WT) and pTRV
plants, all six VIGS plants showed conspicuous symptom of
stunted growth and leaf chlorosis under sodic alkaline stress
(Fig. 4A). When application of melatonin to sodic alkaline-
stressed plants, significantly mitigative effects were shown
in WT, pTRV plants, as well as HBP-1b,bHLH93,ZFP20 and
Fig. 3 Schematic overview of genes exhibiting a change of 2
1
-fold or more in response to melatonin associated with stress response and signaling.
Fold-change in transcript levels is represented by the color scale with darkest red indicating genes with the greatest increase in transcript levels
(2
2
-fold or greater) and darkest blue indicating genes with the greatest decrease in transcript levels (at least 2
2
-fold). Each gene involved in stress
responses is represented once. The detailed information of related DEGs can be observed in Supplementary Table S5.
Table 2 The information of six melatonin-regulated transcription factors
Gene ID Gene name C vs. M C vs. S C vs. SM S vs. SM
RNA-seq qRT-PCR RNA-seq qRT-PCR RNA-seq qRT-PCR RNA-seq qRT-PCR
Solyc02g073580.1 HBP-1b 1.09 1.36 3.19 2.52 1.42 1.15 1.78 1.33
Solyc00g050430.2 bHLH93 10.89 1.26 1.64 n.d. 0.32 1.52 1.43
Solyc03g026270.1 DREB11.67 1.31 n.d. 0.21 2.44 1.98 2.92 2.43
Solyc09g065850.2 IAA3 1.01 0.92 n.d. 1.13 n.d. 1.21 1.19 1.04
Solyc12g008660.1 ZFP20 1.02 0.86 1.82 1.35 n.d. 0.1 1.94 1.65
Solyc02g084590.2 GATA-5 1.09 1.12 n.d. 0.15 1.19 0.93 1.88 1.53
2055
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
GATA-5 VIGS plants. Importantly, melatonin application to
sodic alkaline-stressed plants had nearly no mitigative
effects on DREB1and IAA3 VIGS plants between ‘S’ treatment
and ‘SM’ treatment. These results implied that both DREB1
and IAA3 played essential roles in melatonin-induced sodic al-
kaline stress tolerance in tomato plants. In order to further
confirm this conclusion, a series of parameters including
plant height, dry weight, chlorophyll content, P
N
,F
v
/F
m
, elec-
trolyte leakage and MDA content were determined in
these eight kinds of plants (Fig. 4B–H). As a result, the patterns
of these parameters also aligned well with the phenotypes.
These results suggest that melatonin is capable of inducing
sodic alkaline stress tolerance in tomato, and DREB1and
IAA3 act as downstream signals of melatonin to relieve sodic
alkaline stress.
Melatonin-induced DREB1abinds to the IAA3
promoter to active its transcription
As the key downstream regulators of melatonin-induced sodic
alkaline stress tolerance, we firstly wanted to know how mela-
tonin and stress influenced the gene expression of DREB1and
IAA3, as well as their interaction. As shown in Fig. 5A, B, both
DREB1and IAA3 were significantly induced by ‘M’ in pTRV
roots (P<0.05). However, the upregulation of DREB1began at
3 h after treatment, and the upregulation of IAA3 began at 12 h
after treatment. Similarly, this result was observed in ‘S’-treated
pTRV roots, but which was later and slighter than ‘M’. These
results indicated that the expression of DREB1was induced
earlier by both melatonin and sodic alkaline stress when com-
pared with IAA3. Additionally, melatonin was more effective in
activating the transcription of DREB1and IAA3 when com-
pared with sodic alkaline stress. To our interesting, the time
differences between these two genes’ treatment-responsive
profile led us to consider whether there were some kinds of
interaction between DREB1and IAA3. Then, we designed the
similar qRT-PCR analysis of DREB1expression in pTRV-IAA3
and IAA3 expression in pTRV-DREB1in responding to ‘M’ and
‘S’. Importantly, no significant differences of DREB1expression
were observed in responding to both ‘M’ and ‘S’ between pTRV
and pTRV-IAA3 roots (Fig. 5A;P<0.05). As a comparison, both
‘M’ and ‘S’ induced expressions of IAA3 were significantly in-
hibited by pTRV-DREB1when compared with pTRV control
(Fig. 5B;P<0.05). These results indicated that melatonin or
sodic alkaline stress firstly induced the expression of DREB1,
which played as key activator for IAA3 expression in signaling
transduction.
Fig. 4 (A) Representative phenotypes of sodic alkaline stress mitigation by exogenous melatonin in WT, plants infiltrated by an empty pTRV
vector (pTRV), and six target gene-silenced plants (pTRV-HBP-1b, pTRV-bHLH93, pTRV-DREB1, pTRV-IAA3, pTRV-ZFP20 and pTRV-GATA-5)
10 d after treatment. The influences of melatonin on (B) plant height, (C) dry weight, (D) chlorophyll content, (E) net photosynthetic rate (P
N
),
(F) the maximum PSII quantum yield (F
v
/F
m
), (G) electrolyte leakage and (H) MDA content of all above eight kinds of tomato plants under
control and sodic alkaline stress. Data represent the means of five replicates (±SE), and different letters are significantly different (P<0.05).
2056
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
The above data suggested that IAA3 promoter might be a
candidate of DREB1. To test this hypothesis, the Y1H assay was
conducted to determine whether DREB1acould directly bind
to the promoter of IAA3 (Fig. 5C). The promoter of IAA3 was
cloned in front of a LacZ reporter gene construct as promoter
baits to form reporter construct, and the DREB1coding
sequence was fused with the yeast (Saccharomyces cerevisiae)
GAL4 activation domain (GAD) to form the effector AD-
DREB1aconstruct. Yeast cells containing both the effector
AD-DREB1a(the effector control AD as negative control) and
the reporter constructs will express the GAD-DREB1afusion
protein, and if the DREB1acan bind to the cloned IAA3 pro-
moter sequence of the reporter gene construct, the GAD will be
able to direct LacZ expression, resulting in the blue color accu-
mulation in the presence of substrate 5-bromo-4-chloro-3-
indolyl-b-glucuronic acid. So, the data indicated that IAA3 is
a direct target of DREB1.
Roles of DREB1aand IAA3 in melatonin-induced
sodic alkaline stress
Na
+
accumulation, K
+
deficit and Na
+
/K
+
imbalance are usu-
ally the key problems induced by sodic alkaline stress (Gong
et al. 2014a). As shown in Fig. 6A–C, exogenous application
melatonin had significant effects on decreasing Na
+
accumula-
tion, increasing K
+
accumulation, resulting lower Na
+
/K
+
(P<0.05). However, the effects of exogenous melatonin were
abolished by pTRV-DREB1, pTRV-IAA3 and pTRV-DREB1/
IAA3 (P<0.05). To determine the mechanism, expression
analyses of plasma membrane Na
+
/H
+
antiporter (SOS1), vacu-
olar Na
+
/H
+
exchanger (HKT1 and HKT2) and Na
+
transporter (HKT1,1and HKT1,2) were tested in tomato roots
(Fig. 6D–G). Except SOS1 and HKT1,2expression between
pTRV and pTRV-DREB1, all tested genes were significantly
downregulated by pTRV-DREB1, pTRV-IAA3 and pTRV-
DREB1/IAA3, when compared with pTRV (P<0.05). These
results indicated that SOS1 and HKT1,2were only regulated
by IAA3, and the other three genes were regulated by both
DREB1and IAA3.
Osmosis and drought are typical secondary stresses in sodic
alkaline stress. And DREB family genes are widely involved in
osmotic and droughty stress response. Leaves of pTRV-DREB1,
pTRV-IAA3 and pTRV-DREB1/IAA3 showed significantly
faster water loss rate than pTRV leaves (Fig. 7A; P<0.05),
which indicated that both DREB1and IAA3 had roles in reg-
ulating stomatal closing. Importantly, melatonin-induced de-
crease of stomatal conductance was inhibited by pTRV-
DREB1, pTRV-IAA3 and pTRV-DREB1/IAA3 (Fig. 7B;
P<0.05), resulting significantly lower instantaneous water-
use efficiency (Fig. 7C; P<0.05). These results indicated that
melatonin-induced stomatal closing and high-efficient use of
water depend on DREB1and IAA3 signaling pathway.
Sodic alkaline-stressed plants may enhance organic acid syn-
thesis and secretion to counter the shortage of inorganic anions
and maintain stable intracellular and extracellular pH (Gong
et al. 2014d). We found that exogenous application melatonin
significantly reduced the pH of alkaline culture medium
(Fig. 8A; P<0.05), indicating an active acid secretion of
roots. However, the effects were abolished in pTRV-DREB1,
pTRV-IAA3 and pTRV-DREB1/IAA3 (P<0.05). To reveal the
mechanism, two kinds of key organic acids (malate and citrate)
and acid secretion regulator (plasma membrane H
+
-ATPase;
HA4) were tested in tomato roots (Fig. 8B–D). With similar
analysis as Fig. 6, we found that malate accumulation and HA4
Fig. 5 (A) Effects of melatonin (M) and sodic alkaline stress (S) on
DREB1expression in both pTRV roots and pTRV-IAA3 roots. (B)
Effects of ‘M’ and ‘S’ on IAA3 expression in both pTRV roots and
pTRV-DREB1roots. Data represent the means of five replicates (±
SE). (C) The Y1H assays for the interaction between DREB1aand IAA3
promoter (1500 bp) to direct LacZ expression in yeast cells that
turns 5-bromo-4-chloro-3-indolyl-b-D-galactopyranoside to the blue
compound. Diagram of constructs used in the studies: The GAD
driven by the GAL1 (P
GAL1
) promoter served as negative control to
see if there exists the self-activity of IAA3 promoter; The GAD-
DREB1fusion genes served as effectors; The LacZ gene driven by
IAA3 promoter served as the reporter to test the binding activity of
the GAD-DREB1afusion protein to IAA3 promoter.
2057
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
expression were only regulated by IAA3, and the citrate accu-
mulation was regulated by both DREB1and IAA3.
ROS burst can be found nearly in all stresses, and melatonin
can activate the antioxidant system (Gong et al. 2017). So, we
also analyzed the roles of DREB1and IAA3 in melatonin-
induced ROS detoxification. Using similar analysis as Fig. 6,
we found that ascorbate peroxidase (APX) was only regulated
by IAA3, glutathione peroxidase (GPX) was only regulated by
DREB1, Cu–Zn superoxide dismutase (Cu–Zn SOD) and cata-
lase (CAT) were regulated by both DREB1and IAA3 against
superoxide anion (O
2) and hydrogen peroxide (H
2
O
2
) accu-
mulation in melatonin-induced ROS detoxification pathway
(Fig. 9).
Discussion
Multiple publications showed that melatonin has powerful effects
on alleviating nearly all abiotic stresses (Y. Wang et al. 2018),
including sodic alkaline stress in our previous study (Liu et al.
2015a, Liu et al. 2015b). However, melatonin-induced global
insights and underlying regulatory mechanism in resisting
sodic alkaline stress remain unclear in plants. In the present
study, protective roles of melatonin responding to sodic alka-
line stress were observed in tomato plants (Fig. 1A), as con-
firmed by the lower damage due to NaHCO
3
on shoot and root
growth, as well as photosynthesis and cell damage (Table 1).
Moreover, levels of endogenous melatonin were induced by
both exogenous melatonin and sodic alkaline stress in
tomato roots (Fig. 1B), further suggesting that endogenous
melatonin responding to NaHCO
3
might be related to the
sodic alkaline stress response. Unfortunately, no references
can be found to make sure whether directly absorption or de
novo biosynthesis for increased endogenous melatonin concen-
trations in exogenous melatonin-treated plants. Comparative
omic techniques are frequently used to investigate stress-re-
sponsive mechanisms as well as key regulators in plants (H.
Wang et al. 2018). Numbers of DEGs were significantly reduced
Fig. 6 The influences of melatonin on (A) Na
+
content, (B) K
+
content, (C) Na
+
/K
+
ratio and relative expression of (D) SOS1, (E) NHX1, (F)
NHX2, (G) HKT1,1 and (H) HKT1,2 of pTRV, pTRV-DREB1a, pTRV-IAA3 and pTRV-DREB1a/IAA3 roots under control and sodic alkaline stress.
Data represent the means of five replicates (±SE), and different letters are significantly different (P<0.05).
2058
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
by melatonin under stress condition (Fig. 1C), which indicated
that melatonin played a key role in restoring the sodic alkaline
stress-disturbed gene expression in tomato roots. Similar results
can be obtained from some other omic researches under stress
conditions (Abdelrahman et al. 2018).
Plant growth regulation is mainly depended on hormone
and metabolism and energy conversion, the homeostasis of
which is easily destroyed by stressors (Zhu 2016). KEGG path-
way analysis showed that all seven kinds of hormone metabol-
ism were enhanced in ‘C vs. S’ (Fig. 2). Importantly, the
cytokinin pathway was further enhanced under ‘C vs. SM’,
which implied that melatonin has effects on activating cytoki-
nin signaling pathway against sodic alkaline stress. As common,
when plant root exposing to stress, the cytokinin concentration
decreased, not only in roots, but also in leaves, buds and shoot
tips (O’Brien and Benkova
´2013), which demonstrated that
melatonin-induced cytokinin signaling maybe partly respon-
sible for stress tolerance. Hormone metabolic abundance of
abscisic acid, ethylene, salicylic acid and jasmonic acid was
lower in ‘C vs. SM’ than ‘C vs. S’ (Fig. 2). Though these four
kinds of hormones play important roles in stress tolerance, they
are also known as senescence-related hormones (Verma et al.
2016). So, combining with the phenotype (Fig. 1A), we con-
jectured that the decreased abundance of these four hormones
signaling pathway in ‘C vs. SM’ is more helpful for plant growth
vigor rather than stress tolerance. Thus, melatonin improved
the sodic alkaline stress tolerance through regulating the prof-
itable hormone signaling network. As downstream functional
composition of hormone, metabolism and energy conversion
were also significantly changed by both stress and melatonin.
However, their regulatory genes were usually activated or in-
hibited by hormone-induced transcriptional factors (Puja et al.
2015). Importantly, the transcriptional factors were significantly
enriched in ‘C vs. M’ and ‘S vs. SM’ (Fig. 2), which can be
understood as ‘melatonin effects’ under both control and
sodic alkaline stress conditions. Thus, the enriched metabolism
and energy conversion pathway in ‘C vs. S’ was restored by
melatonin application treatments in ‘C vs. M’, ‘C vs. SM’ and
‘S vs. SM’ (Fig. 2). The present, as well as several previous studies
indicated that metabolism and energy conversion is vulnerable
pathway when plants exposing to sodic alkaline stress (Gong
et al. 2014d, Gong et al. 2015, Li et al. 2018, Sun et al. 2018).
More recently, the melatonin receptor CAND2/PMTR1 has
been identified in Arabidopsis (Wei et al. 2018), which provides
a favorable evidence for the pleiotropic roles of this phytohor-
mone in plants. Because transcriptional factors are important
messengers between phytohormone and metabolic enzymes
(Long and Benfey 2006), we selected these six key transcrip-
tional factors for candidates in the melatonin signaling pathway
(Table 2).
Melatonin-induced stress tolerance is complex, involving
multiple signaling pathways, which regulates many aspects of
morphological, physiological and metabolic processes (Y. Wang
et al. 2018). Using VIGS approach for genetic evidence, we
showed that DREB1and IAA3 were directly integrated into
the melatonin-induced stress tolerance (Fig. 4). More interest-
ing, we found that IAA3 expression was strongly dependent on
DREB1that directly bound to IAA3 promoter to regulate IAA3
expression in responding to exogenous melatonin (Fig. 5). The
DREB gene family consists of 56 members in Arabidopsis were
divided into subfamilies A1–A6 (Nakano et al. 2006). And the
tomato DREB1belongs to DREB A1 subfamilies. As an import-
ant evidence suggesting us, DREB proteins from subfamilies A1,
A4 and A5 displayed a robust interaction with promoters of
IAA3 and IAA5 (Shani et al. 2017). Another evidence for the
involvement of DREB1 in melatonin signaling has been reported
in Arabidopsis for plant abiotic and biotic stresses response (Shi
et al. 2015b, Shi et al. 2016). However, these two studies only
reveal the correlation between melatonin concentration and
DREB1 expression, but the relationship of upstream and down-
stream in melatonin and DREB1 signaling pathway was not
testing by genetic approach. Interestingly, though melatonin
regulates Arabidopsis root system architecture likely acting
Fig. 7 (A) Time course of water loss from the detached leaves of
pTRV, pTRV-DREB1a, pTRV-IAA3 and pTRV-DREB1a/IAA3 plants.
Water loss is expressed as a percentage of the initial fresh weight.
The influences of melatonin on (B) stomatal conductance and (C)
instantaneous water-use efficiency of pTRV, pTRV-DREB1a, pTRV-
IAA3 and pTRV-DREB1a/IAA3 leaves under control and sodic alkaline
stress. Data represent the means of five replicates (±SE), and different
letters are significantly different (P<0.05).
2059
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
auxin signaling independently (Pelagio-Flores et al. 2012). IAA17
has been identified to positively modulate natural leaf senes-
cence through melatonin-mediated pathway in Arabidopsis
(Shi et al. 2015c). In addition, we also provided evidence that
auxin was key hormone involving in sodic alkaline stress toler-
ance in cucumber plants (Gong et al. 2014c). The present study
suggested that IAA3 was one of auxin signaling genes involving
in melatonin-mediated sodic alkaline stress (Figs. 4, 5). The Aux/
IAA proteins, including IAA3 in this study, are known to func-
tion as transcriptional repressors, which implies that the activa-
tion of stress tolerance requires repression of a subset of auxin-
regulated genes (Shani et al. 2017). However, the identification of
these genes is largely unknown at present. So, little is known
about the downstream genes of IAA3 in melatonin-induced
Fig. 9 The influences of melatonin on (A) O
2productivity rate, (B) H
2
O
2
content, and relative expression of (C) Cu–Zn SOD, (D) CAT, (E) APX
and (F) GPX of pTRV, pTRV-DREB1a, pTRV-IAA3 and pTRV-DREB1a/IAA3 roots under control and sodic alkaline stress. Data represent the
means of five replicates (±SE), and different letters are significantly different (P<0.05).
Fig. 8 The influences of melatonin on (A) acid secretion, (B) malate content, (C) citrate content, and (D) relative expression of HA4 of pTRV,
pTRV-DREB1a, pTRV-IAA3 and pTRV-DREB1a/IAA3 roots under control and sodic alkaline stress. Acid secretion is expressed as the pH value of
nutrient solution 3 d after treatment. Data represent the means of five replicates (±SE), and different letters are significantly different (P<0.05).
2060
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
sodic alkaline stress tolerance. However, the upstream of DREB1
has been reported as the ZAT6, which can be directly induced
by melatonin to activate the DREB1 in improving freezing stress
resistance in Arabidopsis (Shi and Chan 2014). As a common
law, plant stress tolerance is usually associated with growth
inhibition. Excepting gibberellic acid, auxin has also been impli-
cated in this inhibition (Naser and Shani 2016). More interest-
ing, there are some evidences pointing to DREB1 cross-linked
signaling pathway in this inhibition (Achard et al. 2008). If the
growth inhibition involves stress tolerance, activation of the
IAAs, including IAA3, may improve stress tolerance. It is possible
that the target genes of IAAs are not only directly associated
with growth but also involved in stress tolerance; because many
auxin-responsive genes are not obviously related to growth
(Chapman et al. 2012). In fact, a recent study in the moss
Physcomitrella patens demonstrated that over one-third of
the genes in genome were regulated by the IAAs (Lavy et al.
2016). Although we have focused on IAA3, it is possible that
other members of the IAAs family are also regulated by DREB1a
proteins. Indeed, in our previous analysis for melatonin-induced
adventitious root generation in tomato plants, 15 of 26 IAAs are
affected by exogenous melatonin treatment in addition to IAA3
(Wen et al. 2016). It will be vital to determine whether these
genes contribute to stress tolerance too, as well as to identify
the downstream targets of these IAAs that contribute to stress
response in the future.
In order to resist sodic alkaline stress, plants have evolved
complex mechanisms to prevent stress-triggered cell damage
and plant inhibition, which mainly involves Na
+
detoxification,
dehydration resistance, high pH buffering and ROS scavenging
(Fig. 10; Gong et al. 2013, Gong et al. 2015, Pang et al. 2016).
Stress signals can be perceived by receptors that are located in
the cell membrane, followed by signal transduction to second-
ary messengers, including hormone, ROS, as well as melatonin
(Shi et al. 2015a). These messengers are involved in stress sen-
sing and signal transduction, leading to the activation of down-
stream transcriptional factors, further regulating various
physiological responses, which ultimately generate protective
responses at the whole plant level (Long and Benfey 2006). The
present study has established several important issues. First,
exogenous melatonin confers enhanced resistance of tomato
plants to sodic alkaline stress (Fig 1). Second, the transcripts of
DREB1and IAA3 can be quickly and remarkably upregulated
by exogenous melatonin treatment (Fig. 5). Moreover, DREB1a
can directly interact with IAA3 promoter to activate the tran-
scripts of IAA3 (Fig. 5). This is the first report that shows the
involvement of cross talk between DREB1and IAA3 in mela-
tonin-induced stress response. Third, mainly sodic alkaline
stress tolerance processes can be regulated, or partly regulated
by the ‘melatonin—DREB1—IAA3’ signaling pathway
(Figs. 6–9). Under excess Na
+
conditions, plants need large
quantity of ATP to keep the homeostasis of Na
+
and K
+
, pro-
mote Na
+
efflux and compartmentalization (Nutan et al. 2018).
To against high pH of sodic alkaline stress, plants can accumu-
late organic acids by altering glycolysis and tricarboxylic acid
cycle pathway, which are carried at the cost of energy (Etienne
et al. 2013, Gong et al. 2014d). Reducing power, including
NADH and NADPH, is also used for enzymatic antioxidant
system-induced ROS scavenging under stress condition
(Pandey et al. 2017). So, the activation of IAA3 may lead to a
suppressed growth phenotype, which can save more energy for
the abovementioned stress resistive processes. Thus, we suggest
the nature that melatonin-induced sodic alkaline stress toler-
ance is flexible and multiple regulation of energy distribution.
And similar opinion, ‘stress signaling in plants evolved from
energy sensing’, was also suggested by Zhu (2016).
In conclusion, the results of this study demonstrated that
DREB1is a key downstream transcriptional factor of mela-
tonin in coordinating the expression of IAA3 to cope with
sodic alkaline stress. As transcriptional factors, DREB1and
IAA3 activated four melatonin-induced physiological processes
against sodic alkaline stress (Fig. 10). However, the ‘mela-
tonin—DREB1—IAA3’ signaling pathway may modulate
energy distribution between growth and resistance through
other unknown pathways. Overall, this study suggested that
DREB1and IAA3 were positive resistant modulators, and pro-
vided a direct link among melatonin, DREB1and IAA3 in the
sodic alkaline stress tolerance activating in tomato plants.
Materials and Methods
Plant materials and treatments
Tomato (Solanum lycopersicum L.) seeds were germinated and then sown in
vermiculite at 25C–28C. After the third true leave emerging, seedlings were
selected and transferred into plastic container filled with 5 L of Hoagland so-
lution (Hoagland and Amon 1950). All containers were brushed with black
paint to protect the exogenous melatonin and roots from light exposure,
and were cultivated in a controlled glasshouse. The glasshouse conditions
were maintained as follows: 22–25C/15–18C (day/night), approximately
75% relative humidity, 12/12 h (light/dark) photoperiod achieved with natural
light and augmented with supplemental lights (400-W high-pressure sodium
lamp, Philips, Amsterdam, the Netherlands), and 1,400 mmols
1
m
2
average
photosynthetic photon flux density across replications for daytime hours. Ten
days after precultivation, the treatments were started. The experiment for
transcriptome included four treatments: (i) control (marked as: C), tomato
plants cultivated with only Hoagland nutrient solution; (ii) melatonin
(marked as: M), Hoagland nutrient solution plus 0.5 mM melatonin; (iii) stress
(marked as: S), Hoagland nutrient solution plus 75 mM NaHCO
3
; (iv) stress with
melatonin (marked as: SM) Hoagland nutrient solution plus 75 mM NaHCO
3
and 0.5 mM melatonin. The experiment was arranged in a randomized complete
block design with five replicates, and the solution was replaced every 2 d.
Virus-induced gene silencing
VIGS was performed by infiltration of tomato plants with a mix of pTRV1- and
pTRV2-carrying Agrobacterium tumefaciens according to our previous study
(Gong et al. 2017). For generating target gene-silenced constructs, the fragment
of the target gene was amplified via PCR with specific primer (Supplementary
Table S1). The PCR fragment was then digested with SacI and XhoI and cloned
into the same sites of pTRV2. All of the constructs were confirmed by sequen-
cing and then transformed into A. tumefaciens strain GV3101. Plants were
infected 3 weeks before they were used for the experiments.
Transcriptome analysis
Total RNA for the transcriptome was obtained from roots of tomato plants 3 d
after treatment using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and sub-
sequently used for mRNA purification and library construction with the
Truseq
TM
RNA Sample Prep Kit (Illumina, San Diego, CA, USA) following the
manufacturer’s instructions. Samples were sequenced on an IlluminaHiSeq
TM
2061
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
2000 (Illumina). Differentially expressed genes were identified using patterns
from gene expression, and functional annotations were assigned according to
Wang et al. (2013).
Photosynthetic apparatus analysis
The third fully expanded leaf of each plant was used to determine the net
photosynthetic rate (P
N
), stomatal conductance and instantaneous water-use
efficiency by a photosynthesis system (LI-6400, Lincoln, NE, USA). Chlorophyll
contents were determined according to previous descriptions (Inskeep and
Bloom 1985). The maximum PSII quantum yield (F
v
/F
m
) was measured on
the third fully expanded leaf after 30 min in the dark using a pulse amplitude
modulated system (Model FMS2, Hansatech Instruments, UK) according to our
previous descriptions (Gong et al. 2013).
Determination of melatonin
Roots were ground to a powder in liquid nitrogen and then extracted with
1.5 ml of chloroform at 4C for 15 h. After centrifugation, the chloroform frac-
tion was evaporated to dryness and dissolved in 100 ml of 42% methanol.
Aliquots of 10 ml were subjected to high-performance liquid chromatography
(HPLC) using a fluorescence detector system (Waters, Milford, MA, USA). The
samples were separated on a Sunfire C18 column (4.6 150 mm; Waters) with
a gradient elution profile (from 42% MeOH to 50% MeOH in 0.1% formic acid-
containing water for 27 min, followed by isocratic elution with 50% MeOH in
0.1% formic acid for 18 min at a flow rate of 0.15 mlmin
1
). Melatonin was
detected at 280 nm excitation and 348 nm emission wavelengths. The mela-
tonin was eluted at 31 min under these conditions (Byeon and Back 2014).
ROS determination and damage assessment
The O
2productivity rate was quantified using the method of hydroxylamine
oxidation (Rauckman et al. 1979). The H
2
O
2
concentration was determined
according to Patterson et al. (1984). Lipid peroxidation was determined in terms
of MDA content and electrolyte leakage according to the method of Cavalcanti
et al. (2004).
Determination of Na
+
and K
+
contents
About 0.2 g of powdered dry tomato tissues in each treatment was digested in a
solution of H
2
SO
4
-H
2
O
2
, and the extract was used to determine Na
+
and K
+
contents, which were determined by a flame photometer (Ma et al. 2015).
Determination of malate and citrate
Quantification of malate and citrate was carried out through HPLC method (Gong
et al. 2014d). Three grams of root samples were ground with 3ml 80% ethyl alcohol.
The mixture was heated at 75C for 30 min, and centrifuged at 8,000gfor 10 min
before transferring the supernatant to a 25-ml volumetric flask. The precipitate was
suspended with 5 ml 80% ethyl alcohol and again centrifuged at 8,000g.The
resulting supernatant was transferred to the same 25-ml volumetric flask, made
up to 25 ml volume with ultrapure water. This solution was evaporated to dryness
in a freeze drier (Speed Vac, Savant Instruments, Holbrook, NY, USA) before being
redissolved with 3 ml ultrapure water. This solution was then filtered with a 0.22-
mm membrane filter. A solution of 10 ml of the filtrate was injected into an HPLC
(waters 510, Waters) that was fitted with a Thermo Hypersil GOLD AQ column
(250 4.6 mm i.d., 5 mm particle size). The mobile phase was 98:2 10 mm
NH
4
H
2
PO
4
(the pH value was adjusted to 2.5 with phosphoric acid): methyl alcohol
(v:v) run at 0.8 mlmin
1
at room temperature. The organic acids were detected at
210 nm with a dual absorbance detector (Waters 2478). A mixed standard so-
lution for malate and citrate was made in ultrapure water at concentrations within
the ranges found in the plant samples. As with the sample solution, 10 mlofthe
mixed standards was run through the HPLC system. Linear standard curves of
malate and citrate were generated from the areas under the peaks corresponding
to the different concentrations. The standard curves were used for the quantifica-
tion of malate and citrate in the samples. To verify the running conditions’ accur-
acy,amixtureofthestandardmalateandcitratewasrunbeforeeachbatchof
samples was analyzed.
Quantitative RT-PCR
Total RNA was extracted using Trizol reagent (Invitrogen). cDNA synthesis was
performed according to standard procedures of Revert Aid First Strand cDNA
Fig. 10 Proposed model for melatonin-induced sodic alkaline stress tolerance.
2062
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
Synthesis Kit (Fermentas). qRT-PCR was performed with the primers in
Supplementary Table S2 to detect the level of expression of target genes and
the control gene Actin. At least three technical replicate qRT-PCR reactions
were performed per primer pair using an aliquot of cDNA (1/500th), Power
SYBR Green PCR Master Mix (Applied Biosystems; ABI) and 200 nM of each
primer on an ABI Prism 7900 HT machine (ABI). Data were analyzed with the
SDS 2.0 software (ABI), and relative expression was calculated using the com-
parative cycle threshold method (Pfaffl 2001) with normalization of data to the
geometric average of the internal control genes (Vandesompele et al. 2002).
Yeast one-hybrid assay
Yeast one-hybrid (Y1H) assays were performed as described by Zhang and Gan
(2012). Plasmid for GAD::DREB1fusion (pGL3175) was cotransformed with
LacZ reporter gene constructs containing IAA3 promoter fragments into the
yeast strain EGY48 using standard transformation techniques. Transformants
were grown on proper drop-out plates containing 5-bromo-4-chloro-3-indolyl-
b-D-galactopyranoside for the blue color development.
Statistical analysis
The statistical analysis was performed using the SAS 9.0 statistical software
package (SAS Institute, Cary, NC, USA). The differences between treatments
were determined by the LSD test, and P<0.05 was taken to indicate statistical
significance.
Supplementary Data
Supplementary data are available at PCP online.
Funding
The National Natural Science Foundation of China [31872954
and 31872943]; the National Key Research and Development
Program of China [2018YFD1000800]; the Shandong Provincial
Natural Science Foundation, China [ZR2019MC067]; the
Shandong Province Modern Agricultural Technology System
(SDAIT-05–05); the Project from State Key Laboratory of
Crop Biology [dxkt201714]. We thank Prof. Yujin Hao
(Shandong Agricultural University) for providing the TRV
vector.
Disclosures
The authors have no conflicts of interest to declare.
References
Abdelrahman, M., Jogaiah, S., Burritt, D.J. and Tran, L.S.P. (2018) Legume
genetic resources and transcriptome dynamics under abiotic stress con-
ditions. Plant Cell Environ. 41: 1972–1983.
Achard, P., Gong, F., Cheminant, S., Alioua, M., Hedden, P. and Genschik, P.
(2008) The cold-inducible CBF1 factor-dependent signaling pathway
modulates the accumulation of the growth-repressing DELLA proteins
via its effect on gibberellin metabolism. Plant Cell 20: 2117–2129.
Bonnefond, A., Cle
´ment, N., Fawcett, K., Yengo, L., Vaillant, E., Guillaume,
J.L., et al. (2012) Rare MTNR1B variants impairing melatonin receptor 1B
function contribute to type 2 diabetes. Nat. Genet. 44: 297–303.
Byeon, Y. and Back, K. (2014) An increase in melatonin in transgenic rice
causes pleiotropic phenotypes, including enhanced seedling growth,
delayed flowering, and low grain yield. J. Pineal Res. 56: 408–414.
Cai, S.Y., Zhang, Y., Xu, Y.P., Qi, Z.Y., Li, M.Q., Ahammed, G.J., et al. (2017)
HsfA1a upregulates melatonin biosynthesis to confer cadmium toler-
ance in tomato plants. J. Pineal Res. 62: e12387.
Cavalcanti, F.R., Oliveira, J.T.A., Martins-Miranda, A.S., Vie
´gas, R.A. and
Silveira, J.A.G. (2004) Superoxide dismutase, catalase and peroxidase
activities do not confer protection against oxidative damage in salt-
stressed cowpea leaves. New Phytol. 163: 563–571.
Chapman, E.J., Greenham, K., Castillejo, C., Sartor, R., Bialy, A., Sun, T.P.,
et al. (2012) Hypocotyl transcriptome reveals auxin regulation of
growth-promoting genes through GA-dependent and -independent
pathways. PLoS One 7: e36210.
Debnath, B., Hussain, M., Irshad, M., Mitra, S., Li, M., Liu, S., et al. (2018)
Exogenous melatonin mitigates acid rain stress to tomato plants
through modulation of leaf ultrastructure, photosynthesis and antioxi-
dant potential. Molecules 23: 1–15.
Dubbels, R., Reiter, R.J., Klenke, E., Goebel, A., Schnakenberg, E., Ehlers, C.,
et al. (1995) Melatonin in edible plants identified by radioimmunoassay
and by high performance liquid chromatography-mass spectrometry.
J. Pineal Res. 18: 28–31.
Etienne, A., Ge
´nard, M., Lobit, P., Mbeguie, A., Mbeguie, D. and Bugaud, C.
(2013) What controls fleshy fruit acidity? A review of malate and citrate
accumulation in fruit cells. J. Exp. Bot. 64: 1451–1469.
Fan, J.B., Xie, Y., Zhang, Z.C. and Chen, L. (2018) Melatonin: a multifunc-
tional factor in plants. Int. J. Mol. Sci. 19: 1–14.
Gong, B., Li, X., Bloszies, S., Wen, D., Sun, S.S., Wei, M., et al. (2014a) Sodic
alkaline stress mitigation by interaction of nitric oxide and polyamines
involves antioxidants and physiological strategies in Solanum lycopersi-
cum.Free Radic. Biol. Med. 71: 36–48.
Gong, B., Li, X., Vandenlangenberg, K.M., Wen, D., Sun, S.S., Wei, M., et al.
(2014b) Overexpression of S-adenosyl-L-methionine synthetase
increased tomato tolerance to alkali stress through polyamine metab-
olism. Plant Biotechnol. J. 12: 694–708.
Gong, B., Miao, L., Kong, W.J., Bai, J.G., Wang, X.F., Wei, M., et al. (2014c) Nitric
oxide, as a downstream signal, plays vital role in auxin induced cucumber
tolerance to sodic alkaline stress. Plant Physiol. Biochem. 83: 258–266.
Gong, B., Wen, D., Bloszies, S., Li, X., Wei, M., Yang, F.J., et al. (2014d)
Comparative effects of NaCl and NaHCO
3
, stresses on respiratory me-
tabolism, antioxidant system, nutritional status, and organic acid me-
tabolism in tomato roots. Acta Physiol. Plant. 36: 2167–2181.
Gong, B., Wen, D., Vandenlangenberg, K., Wei, M., Yang, F.J., Shi, Q.H., et al.
(2013) Comparative effects of NaCl and NaHCO
3
, stress on photosyn-
thetic parameters, nutrient metabolism, and the antioxidant system in
tomato leaves. Sci. Hortic. 157: 1–12.
Gong, B., Wen, D., Wang, X.F., Wei, M., Yang, F.J., Li, Y., et al. (2015) S-
nitrosoglutathione reductase-modulated redox signaling controls sodic
alkaline stress responses in Solanum lycopersicum L. Plant Cell Physiol.
56: 790–802.
Gong, B., Yan, Y.Y., Wen, D. and Shi, Q.H. (2017) Hydrogen peroxide
produced by NADPH oxidase: a novel downstream signaling pathway
in melatonin-induced stress tolerance in Solanum lycopersicum.Physiol.
Plant. 160: 396–409.
Gong, B., Zhang, C.J., Li, X., Wen, D., Wang, S.S., Shi, Q.H., et al. (2014)
Identification of NaCl and NaHCO
3
stress responsive proteins in
tomato roots using iTRAQ-based analysis. Biochem. Biophys. Res.
Commun. 446: 417–422.
Hoagland, D.R. and Amon, D.I. (1950) The water-culture method for grow-
ing plants without soil. Calif. Agric. Exp. Stn. Circ. 347: 1–32.
Inskeep, W.P. and Bloom, P.R. (1985) Extinction coefficients of chlorophyll a and
b in N, N-dimethylformamide and 80% acetone. Plant Physiol. 77: 483–485.
Lavy, M., Prigge, M.J., Tao, S., Shain, S., Kuo, A., Kirchsteiger, K., et al. (2016)
Constitutive auxin response in Physcomitrella reveals complex inter-
actions between Aux/IAA and ARF proteins. eLife 5: 1–22.
Li, N., Liu, H.L., Sun, J., Zhang, H.L., Wang, J.G., Yang, L.M., et al. (2018)
Transcriptome analysis of two contrasting rice cultivars during alkaline
stress. Sci. Rep. 8: 1–16.
2063
Plant Cell Physiol. 60(9): 2051–2064 (2019) doi:10.1093/pcp/pcz126
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
Liu, N., Gong, B., Jin, Z.Y., Wang, X.F., Wei, M., Yang, F.J., et al. (2015a) Sodic
alkaline stress mitigation by exogenous melatonin in tomato needs
nitric oxide as a downstream signal. J. Plant Physiol. 186: 68–77.
Liu, N., Jin, Z., Wang, S.S., Gong, B., Wen, D., Wang, X.F., et al. (2015)
Sodic alkaline stress mitigation with exogenous melatonin involves re-
active oxygen metabolism and ion homeostasis in tomato. Sci. Hortic.
181: 18–25.
Long, T.A. and Benfey, P.N. (2006) Transcription factors and hormones:
new insights into plant cell differentiation. Curr. Opin. Cell Biol. 18: 710–
714.
Ma, Y.C., Wang, J.Y., Zhong, Y., Geng, F., Cramer, G.R. and Cheng, Z.M.
(2015) Subfunctionalization of cation/proton antiporter 1 genes in
grapevine in response to salt stress in different organs. Hortic. Res.2:
1–9.
Martinez, V., Nieves-Cordones, M., Lopez-Delacalle, M., Rodenas, R.,
Mestre, T., Garcia-Sanchez, F., et al. (2018) Tolerance to stress combin-
ation in tomato plants: new insights in the protective role of melatonin.
Molecules 23: 1–20.
Nakano, T., Suzuki, K., Fujimura, T. and Shinshi, H. (2006) Genome-wide
analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol.
140: 411–432.
Naser, V. and Shani, E. (2016) Auxin response under osmotic stress. Plant
Mol. Biol. 91: 661–672.
Nutan, K.K., Kumar, G., Singla-Pareek, S.L. and Pareek, A. (2018) A salt
overly sensitive pathway member from Brassica juncea BjSOS3 can
functionally complement DAtsos3 in Arabidopsis. Curr. Genomics 19:
60–69.
O’Brien, J.A. and Benkova
´, E. (2013) Cytokinin cross-talking during biotic
and abiotic stress responses. Front. Plant Sci. 4: 1–11.
Pandey, S., Fartyal, D., Agarwal, A., Shukla, T., James, D., Kaul, T., et al.
(2017) Abiotic stress tolerance in plants: myriad roles of ascorbate
peroxidase. Front. Plant Sci. 8: 1–13.
Pang, Q., Zhang, A., Zang, W., Wei, L. and Yan, X.F. (2016) Integrated
proteomics and metabolomics for dissecting the mechanism of global
responses to salt and alkali stress in Suaeda corniculata.Plant Soil 402:
1–16.
Patterson, B.D., Macrae, E.A. and Ferguson, I.B. (1984) Estimation of hydro-
gen peroxide in plant extracts using titanium (IV). Anal. Biochem. 139:
487–492.
Pelagio-Flores, R., Mun
˜oz-Parra, E., Ortiz-Castro, R. and Lo
´pez-Bucio, J.
(2012) Melatonin regulates Arabidopsis root system architecture
likely acting independently of auxin signaling. J. Pineal Res. 538: 279–
288.
Pfaffl, M.W. (2001) A new mathematical model for relative quantification
in real-time RT-PCR. Nucleic Acids Res. 29: 1–6.
Puja, O., Renu, B., Sha, B. and Ravinderjit, K. (2015) The common molecular
players in plant hormone crosstalk and signaling. Curr. Protein Pept. Sci.
16: 369–388.
Rauckman, E.J., Rosen, G.M. and Kitchell, B.B. (1979) Superoxide radical as
an intermediate in the oxidation of hydroxylamines by mixed function
amine oxidase. Mol. Pharmacol. 15: 131–137.
Saito, T. and Matsukura, C. (2015) Effect of salt stress on the growth and
fruit quality of tomato plants. In Abiotic Stress Biology in Horticultural
Plants. Edited by Kanayama, Y. and Kochetov, A. pp. 3–16. Springer,
Tokyo.
Shani, E., Salehin, M., Zhang, Y., Sanchez, S.E., Doherty, C., Wang, R., et al.
(2017) Plant stress tolerance requires auxin-sensitive Aux/IAA tran-
scriptional repressors. Curr. Biol. 27: 437–444.
Shi, H. and Chan, Z. (2014) The cysteine2/histidine2-type transcription
factor zinc finger of Arabidopsis thaliana 6-activated C-repeat-binding
factor pathway is essential for melatonin-mediated freezing stress re-
sistance in Arabidopsis. J. Pineal Res. 57: 185–191.
Shi, H., Jiang, C., Ye, T., Tan, D.X., Reiter, R.J., Zhang, H., et al. (2015)
Comparative physiological, metabolomic, and transcriptomic analyses
reveal mechanisms of improved abiotic stress resistance in bermuda-
grass [Cynodon dactylon (L). Pers.] by exogenous melatonin. J. Exp. Bot.
66: 681–694.
Shi, H., Qian, Y., Tan, D.X., Reiter, R.J. and He, C. (2015) Melatonin induces
the transcripts of CBF/DREB1s and their involvement in both abiotic
and biotic stresses in Arabidopsis. J. Pineal Res. 59: 334–342.
Shi, H., Reiter, R.J., Tan, D.X. and Chan, Z.L. (2015) Indoie-3-acetic acid
inducible 17 positively modulates natural leaf senescence through
melatonin-mediated pathway in Arabidopsis. J. Pineal Res. 58: 26–33.
Shi, H., Tan, D.X., Reiter, R.J., Ye, T.T., Yang, F. and Chan, Z.L. (2015)
Melatonin induces class A1 heat-shock factors (HSFA1s) and their pos-
sible involvement of thermotolerance in Arabidopsis. J. Pineal Res. 58:
335–342.
Shi, H., Wei, Y. and He, C. (2016) Melatonin-induced CBF/DREB1s, are
essential for diurnal change of disease resistance and CCA1, expression
in Arabidopsis. Plant Physiol. Biochem. 100: 150–155.
Sun, Y.F., Ou, Y.B., Gao, Y.F., Zhang, X., He, Y.M., Li, Y., et al. (2018) Different
tolerance mechanism to alkaline stresses between Populus bolleana and
its desert relative Populus euphratica.Plant Soil 426: 349–363.
Tan, D.X. and Reiter, R.J. (2019) Mitochondria: the birth place, battle
ground and the site of melatonin metabolism in cells. Melatonin Res.
2: 44–66.
Vandesompele, J., Preter, K.D., Pattyn, F., Poppe, B., Roy, N.V., Paepe, A.D.,
et al. (2002) Accurate normalization of real-time quantitative RT-PCR
data by geometric averaging of multiple internal control genes. Genome
Biol. 3: RESEARCH0034.
Verma, V., Ravindran, P. and Kumar, P. (2016) Plant hormone-mediated
regulation of stress responses. BMC Plant Biol. 16: 1–10.
Wang, H., Chang, X., Lin, J., Chang, Y.H., Chen, J.C., Reid, M.S., et al. (2018)
Transcriptome profiling reveals regulatory mechanisms underlying cor-
olla senescence in Petunia.Hortic. Res. 5: 1–13.
Wang, L., Feng, C., Zheng, X., Guo, Y., Zhou, F., Shan, D., et al. (2017) Plant
mitochondria synthesize melatonin and enhance the tolerance of
plants to drought stress. J. Pineal Res. 63: e12429.
Wang, Y., Reiter, R.J. and Chan, Z. (2018) Phytomelatonin: a universal
abiotic stress regulator. J. Exp. Bot. 69: 963–974.
Wang, Y., Tao, X., Tang, X.M., Xiao, L., Sun, J.L., Yan, X.F., et al. (2013)
Comparative transcriptome analysis of tomato (Solanum lycopersicum)
in response to exogenous abscisic acid. BMC Genomics 14: 841.
Wei, J., Li, D.X., Zhang, J.R. and Chen, Q. (2018) Phytomelatonin receptor
PMTR1-mediated signaling regulates stomatal closure in Arabidopsis
thaliana.J. Pineal Res. 65: 1–13.
Wei, Y., Hu, W., Wang, Q., Zeng, H., Li, X., Yan, Y., et al. (2017) Identification,
transcriptional and functional analysis of heat-shock protein 90s in
banana (Musa acuminata L.) highlight their novel role in melatonin-
mediated plant response to Fusarium wilt.J. Pineal Res. 62: e12367.
Wen, D., Gong, B., Sun, S.S., Liu, S.Q., Wang, X.F., Wei, M., et al. (2016)
Promoting roles of melatonin in adventitious root development of
Solanum lycopersicum L. by regulating auxin and nitric oxide signaling.
Front. Plant Sci. 7: 1–11.
Xu, L., Yue, Q., Xiang, G., Bian, F. and Yao, Y. (2018) Melatonin promotes
ripening of grape berry via increasing the levels of ABA, H
2
O
2
, and
particularly ethylene. Hortic. Res. 5: 1–16.
Zhang, H.M. and Zhang, Y. (2014) Melatonin: a well-documented antioxi-
dant with conditional pro-oxidant actions. J. Pineal Res. 57: 131–146.
Zhang, K. and Gan, S.S. (2012) An abscisic acid-AtNAP transcription factor-
SAG113 protein phosphatase 2C regulatory chain for controlling dehy-
dration in senescing Arabidopsis leaves. Plant Physiol. 158: 961–969.
Zhu, J.K. (2016) Abiotic stress signaling and responses in plants. Cell 167:
313–324.
2064
Y. Yan et al. |DREB1and IAA3 in melatonin signaling
Downloaded from https://academic.oup.com/pcp/article/60/9/2051/5527762 by guest on 20 October 2022
