A stress inducible SUMO conjugating enzyme gene (SaSce9) from a grass halophyte Spartina alterniflora enhances salinity and drought stress tolerance in Arabidopsis
© Karan and Subudhi; licensee BioMed Central Ltd. 2012
Received: 6 May 2012
Accepted: 5 October 2012
Published: 10 October 2012
SUMO (Small Ubiquitin related Modifier) conjugation is a post translational regulatory process found in all eukaryotes, mediated by SUMO activating enzyme, SUMO conjugating enzyme, and SUMO ligase for the attachment of SUMO to its target protein. Although the mechanism for regulation of SUMO conjugation pathway genes under abiotic stress has been studied to certain extent, the role of SUMO conjugating enzyme in improving abiotic stress tolerance to plant is largely unexplored. Here, we have characterized a SUMO conjugating enzyme gene ‘SaSce9’ from a halophytic grass Spartina alterniflora and investigated its role in imparting abiotic stress tolerance.
SaSce9 gene encodes for a polypeptide of 162 amino acids with a molecular weight of ~18 kD and isoelectric point 8.43. Amino acid sequence comparisons of SaSce9 with its orthologs from other plant species showed high degree (~85-93%) of structural conservation among each other. Complementation analysis using yeast SCE mutant, Ubc9, revealed functional conservation of SaSce9 between yeast and S. alterniflora. SaSce9 transcript was inducible by salinity, drought, cold, and exogenously supplied ABA both in leaves and roots of S. alterniflora. Constitutive overexpression of SaSce9 in Arabidopsis through Agrobacterium mediated transformation improved salinity and drought tolerance of Arabidopsis. SaSce9 overexpressing Arabidopsis plants retained more chlorophyll and proline both under salinity and drought stress. SaSce9 transgenic plants accumulated lower levels of reactive oxygen under salinity stress. Expression analysis of stress responsive genes in SaSce9 Arabidopsis plants revealed the increased expression of antioxidant genes, AtSOD and AtCAT, ion antiporter genes, AtNHX1 and AtSOS1, a gene involved in proline biosynthesis, AtP5CS, and a gene involved in ABA dependent signaling pathway, AtRD22.
These results highlight the prospect of improving abiotic stress tolerance in plants through genetic engineering of the sumoylation pathway. The study provides evidence that the overexpression of SaSce9 in plant can improve salinity and drought stress tolerance by protecting the plant through scavenging of ROS, accumulation of an osmolyte, proline, and expression of stress responsive genes. In addition, this study demonstrates the potential of the halophyte grass S. alterniflora as a reservoir of abiotic stress related genes for crop improvement.
KeywordsAbiotic stress tolerance Halophyte Stress inducible SUMO conjugating gene Spartina alterniflora
Plants are constantly challenged by a wide range of environmental stresses such as drought, high salinity, and temperature fluctuations due to their sessile nature. Response to abiotic stresses is very complex, as various stages of plant growth and development can be affected by a particular stress and often several stresses simultaneously . Molecular responses to abiotic stresses include stress perception, signal transduction to cellular components, gene expression, and metabolic changes, which help the plants to adapt to stress environments [2, 3].
Post-translational modifications of proteins play an important role in most cellular processes by rapidly altering the functions of preexisting proteins and protein complexes. Sumoylation or SUMO (Small Ubiquitin related Modifier) conjugation is one of the essential post translational regulatory process essentially found in all eukaryotes. It is a three step enzymatic cascade mediated by SUMO activating enzyme (E1 or SAE), SUMO conjugating enzyme (E2 or SCE), and SUMO ligase (E3) for the attachment of SUMO to its target protein [4, 5]. SUMO plays an important role in regulation of protein–protein interactions and subcellular locations in yeast and animals [6–8]. Increased level of SUMO conjugates in response to heat shock, oxidative stress, and DNA damaging agents has been reported in mammalian cell cultures [9–12]. Similarly, increased accumulation of SUMO conjugates upon exposure of Arabidopsis seedlings to heat shock, H2O2, ethanol, and amino acid analog canavanine suggests its important role in stress response and protection in plants . Several studies in Arabidopsis highlighted the importance of sumoylation in post translational regulation in response to stresses such as salt, cold, drought, heat, copper toxicity, and nutrient deprivation [14–18]. Importance of sumoylation for abiotic stress response is strengthened from the reports on drastic reduction in tolerance to stresses due to mutation of genes involved in SUMO conjugation [14–16, 19]. Further, embryo lethality caused by insertional mutation in AtSAE2 or AtSCE1 or double mutations in AtSUMO1 and AtSUMO2 genes of Arabidopsis inferred its role in plant growth and development .The reversible conjugation of the SUMO peptide to protein substrates is emerging as a major post-translational regulatory process in plants . Arabidopsis SUMO and related enzymes have been implicated in abscisic acid (ABA) responses, flowering time regulation as well as stress responses . In rice (Oryza sativa), transcripts for the SCE is regulated by cold, salt, ABA, and heat [21, 22]. However, detailed understanding of SCE for abiotic stress tolerance in plant is still in its infancy.
Spartina alterniflora, a halophytic grass commonly known as smooth cordgrass, possesses all the known mechanisms of salt tolerance . In this investigation, we have functionally characterized a SCE gene, SaSce9, previously obtained from the salinity stressed cDNA library of Spartina alterniflora. SaSce9 is a functional homolog of SUMO conjugating enzyme, Ubc9 of Saccharomyces cerevisiae. Salt, drought, cold, and ABA induced the expression of SaSce9 in leaves and roots of Spartina alterniflora. Furthermore, SaSce9 overexpression in Arabidopsis improved abiotic stress tolerance by regulating the stress responsive genes involved in ion homeostasis, proline accumulation, and detoxification of reactive oxygen radicals. This study demonstrates the potential and superiority of orthologous stress responsive genes from a halophyte grass Spartina alterniflora in improving salt and drought stress tolerance in plants.
SaSce9 of spartina alterniflorais an ortholog of SUMO conjugating enzyme
SaSce9 Functionally complemented Ubc9 mutant of saccharomyces cerevisiae
Regulation of expression of SaSce9 by multiple stresses in spartina alterniflora
Overexpression of SaSce9improved salinity tolerance
Overexpression of SaSce9improved drought tolerance
SaSce9Reduced reactive oxygen species (ROS) under drought stress
Expression pattern of stress-responsive genes in SaSce9 transgenic Arabidopsis
Stress responsive genes and their functions
AtNHX1 (vacuolar Na+/H+ antiporter)
Compartmentalization of the excessive Na+ into vacuole
AtSOS1 (plasma membrane Na+/H+ antiporter)
Na+ extrusion from cytosol to surrounding medium
AtP5CS (delta-1-pyrroline-5-carboxylate synthase)
AtRD22 (responsive to dehydration)
Drought stress responsive gene
AtSOD1 (superoxide dismutase)
Decomposition of superoxide into hydrogen peroxide
Decomposition of hydrogen peroxide into water and oxygen
Sumoylation pathway is involved in post translational modification of proteins through employment of three key enzymes, SUMO activating enzyme (E1), SUMO conjugating enzyme (SCE or E2), and SUMO ligase (E3) by regulating gene expression, nuclear localization, and signal transduction [13, 20]. Sumoylation pathway begins with the activation of the SUMO C-terminus through exposing glycine by a SUMO-specific E1 activating enzyme. Activated SUMO is subsequently transferred to the cysteine residue of a SUMO-conjugating enzyme E2, and then with the help of an E3 ligase, SUMO is finally conjugated to the target lysine residue of a substrate protein [5, 34]. In Arabidopsis, sumoylation of proteins has been reported in environmental response, flowering time regulation, and phosphorus starvation [13, 14, 16, 19, 35–37]. Members of sumoylation pathway such as AtSCE1 (SUMO conjugating enzyme), AtSIZ1 (SUMO ligase), AtSUMO1and AtSUMO2 have been identified and found to be involved in ABA signaling and drought response in Arabidopsis[14, 16, 35]. In rice, regulation of SUMO conjugating enzyme genes by temperature stress has also been reported . But whether SUMO conjugating enzyme imparts stress tolerance to plant is still not clear. In this study, we characterized a SUMO conjugating enzyme gene “SaSce9” from a halophytic grass, Spartina alterniflora, and investigated its role in abiotic stress tolerance mechanisms in plant.
SaSce9, an ortholog of SCE, induced by multiple stresses in halophytic grass Spartina alterniflora
We have identified a SUMO conjugating enzyme gene, SaSce9 from Spartina alterniflora, which has same sequence characteristics as the reported yeast SUMO conjugating enzyme, Ubc9. The deduced protein sequence analysis of this gene revealed the presence of high structural homology with SCE orthologs from amoeba, yeast, and plants, suggesting evolutionary conserved function of SCE across the eukaryotes. Predicted tertiary structure of SaSce9 using SWISS-MODEL software suggested the presence of four alpha helices and four beta sheets similar to the known X-ray crystal structure of SCE, HsSce9 of human . To further validate the functionally conserved role of SaSce9, a temperature sensitive mutant strain of Saccharomyces cerevisiae, Ubc9-ts was used . SaSce9 was able to functionally complement the Ubc9 mutant of yeast, indicating the potential evolutionary conserved function of SaSce9 between Spartina and yeast. There are several reports for functional complementation of Ubc9 mutant phenotype by expression of DmUbc9 from D. melanogaster, NbUbc9 from N. benthamiana, HsUbc9 from H. sapiens, and OsSce1 from O. sativa.
Sumoylation status of the proteins involved in stress response is reported to be altered as they travel between the nucleus and the cytosol [13, 17]. As the SaSce9 gene was obtained from salinity stressed library of Spartina alterniflora, we further wanted to check its organ specific inducibility in leaves and roots of Spartina alterniflora under salt, drought, cold, and exogenously supplied ABA stress. Interestingly, the increased expression of SaSce9 transcript was observed under all the stresses, as shown by qRT-PCR, with highest early induction (30 min) found in leaf by salinity and drought and in root by drought and ABA, suggesting the stress responsive transcript accumulation of SaSce9 in Spartina alterniflora. The inducibility of SaSce9 gene by ABA indicated that the expression of SaSce9 may be regulated through ABA responsive pathway in Spartina alterniflora. ABA mediates the responses of plant to stress conditions such as salinity, drought, and cold [41, 42]. Moreover, salt, cold, and ABA stress induced accumulation of SUMO conjugates and high expression of AtSCE1a has been observed in different tissues of Arabidopsis. OsSce1 was found to be induced by temperature stress in the seedlings of rice . Chaikam and Karlson  reported developmental and stress responsive regulation of SUMO cascade components with highest level of expression in reproductive tissues suggesting possible role of sumoylation during flowering in rice.
SaSce9 enhances salinity and drought tolerance in Arabidopsis
Considering the stress inducible response of SaSce9 in Spartina alterniflora, SaSce9 gene was further tested for its role in-planta towards abiotic stress. Under normal condition, growth and morphology of WT, SaSce9 transgenic lines were similar. Under 150 mM NaCl stress, both transgenic lines could grow and set seed successfully, while most of the WT plants died. Higher K+/Na+ ratio in SaSce9 transgenic lines under non-stress and salinity stress suggested improved basal uptake of K+ due to overexpression of SaSce9. Several studies have demonstrated the importance of increased K+/Na+ ratio for tolerance of plants against salinity stress [43–46]. Enhanced expression of two ion transporters, AtNHX1 and AtSOS1, in SaSce9 transgenic plants compared to WT thus confirmed our hypothesis for the preferential uptake of K+ by SaSce9 transgenic plants. Under continuous drought stress, SaSce9 transgenic plants were healthy, turgid, and green, while WT plants lost its vigor and growth. SaSce9 expression improved drought tolerance of SaSce9 Arabidopsis by maintaining membrane stability as its electrolyte leakage was lower than the WT. Retention of chlorophyll in plants under stress is an important aspect for increased stress tolerance. This study demonstrated that the increased level of chlorophyll under salinity and drought stresses might be an important mechanism for the improvement of stress tolerance due to expression of SaSce9 in Arabidopsis.
SaSce9enhances abiotic stress tolerance through scavenging oxygen radicals and proline production
Proline plays a vital role in maintaining osmotic balance and stabilizing cellular structures in plants [30, 47, 48]. Increased free proline content in transgenic Arabidopsis under salinity and drought stress conditions indicated the role of SaSce9 in proline accumulation, thereby protecting the plants against the stress. Enhanced expression of P5CS1 (the key gene involved in proline biosynthesis) in SaSce9 plants compared to the WT plants further supported our hypothesis for the role of SaSce9 in osmotic stress tolerance. In an earlier report, transgenic plants overexpressing the P5CS gene from Vigna aconitifolia accumulated more proline and were more tolerant to osmotic stress . Furthermore, histochemical staining of leaves using NBT showed that even without stress O2- could be stained, but the transgenic lines had lower levels of ROS (reactive oxygen species) relative to WT. Drought stress resulted in increased ROS levels in WT but transgenic lines accumulated remarkably less O2- as evidenced by the accumulation of less blue products. ROS were produced in both non-stress and stress conditions but the balance between the production and removal of ROS determines its effect on cellular system [30, 32, 33]. Plants evolve a complex antioxidant system in order to detoxify stress-induced ROS in which ROS scavenging enzymes such as superoxide dismutase and peroxidase play essential role . Increased expression of AtSOD1 and AtCAT in SaSce9 transgenic plants might be responsible for scavenging ROS produced under drought stress in this study. These analyses further validated the role of SaSce9 for improving stress tolerance in plant by affecting different stress related pathways. Our observation clearly showed the indirect role of SaSce9 in scavenging of oxygen radicals resulting in protection of plant against osmotic stress.
This study demonstrated for the first time that manipulation of a SaSce9 gene, a member of the sumoylation pathway, through transgenic approach, can lead to improved abiotic stress tolerance in plants. Although, Lois et al., developed AtSce1a expressing transgenic Arabidopsis plants, the focus of their study was to correlate the level of AtSce1a expression with the level of sumoylation which in turn attenuates ABA-mediated growth inhibition and induces ABA- and stress-responsive genes. Thus, we hypothesize that overexpression of SaSce9 might have increased the sumoylation status in SaSce9 transgenic plants and improved the stress tolerance by regulating stress responsive genes. Further investigations on identifying interacting partner(s) of sumoylation pathway members and its target protein by comparing SCE mutant would reveal the exact molecular mechanisms for possible role in imparting stress tolerance through manipulation of post translational modifications in plant.
Spartina alternifloraplants and stress treatment
Young (three to four-leaf stage) uniform, clonally propagated plants of Spartina alterniflora cv. ‘Vermilion’ grown in sand-filled plastic pots under normal growth conditions inside a greenhouse with 14 h light and 10 h dark at 26/18°C day/night temperature were used for stress related experiments . Pots were supplied with Hoagland’s nutrient solution . Salinity stress was imposed by using a 5% (w/v) solution of commercial synthetic sea salts (Instant Ocean, Aquarium Systems, Mentor, OH, USA) dissolved in Hoagland’s solution, which is equivalent to the salt concentration of sea water (~35 parts per thousand). Drought stress was imposed by keeping uprooted uniform Spartina plants on Whatman paper under normal growth condition of greenhouse. For cold stress, pots containing plants were kept at 4°C under dim light. For ABA treatment, plants were supplied with 100 μM ABA (Sigma, USA). Leaf and root tissues were collected at different time intervals of stress i.e. 30 min, 1 h, 8 h, 24 h, 48 h, and 72 h from three representative plants. Both root and leaf tissues were thoroughly washed, wiped with tissue paper, immediately frozen in liquid nitrogen, and stored at −80°C till further use. Unstressed plants were harvested as control.
An expressed sequence tag #968 (EST) of Spartina alterniflora from a salinity stressed EST library constructed previously in our laboratory  was found to be similar with SUMO conjugate enzyme gene and was referred as ‘SaSce9’ in this report. It was used for multiple sequence alignment with orthologs from different organisms. Multiple alignments of SaSce9 were performed using ClustalW program  using amino acids, and phylogenetic analyses were conducted in MEGA 4 . Phylogenetic tree of these sequences were inferred using the Neighbor-Joining method . The bootstrap consensus tree inferred from 1,000 replicates was used to represent the evolutionary history of the selected eukaryotic species. The tertiary structure of SaSce9 was predicted by homology modeling based on crystallographic data deposited on the Swissprot using SWISS-MODEL .
Complete open reading frame (ORF) of SaSce9 was PCR amplified using forward primer, SaSce9NheIF and reverse primer, SaSce9BamHIR containing NheI and BamHI restriction endonuclease (RE) sites, respectively (Table 1) and ligated into the NheI and BamHI cloning site of yeast expression vector pVTL260 to generate pVTL260-SaSce9 plasmid. The recombinant clone was confirmed by restriction analysis and DNA sequencing. Plasmid pVTL260 obtained from EUROSCARF (Frankfurt, Germany) has leu2d as the selectable marker and it uses the yeast ADH1 promoter and terminator for expression in yeast. For complementation, Ubc9-ts temperature sensitive yeast mutant, YWO103 [MAT α ubc9-TRP1, his3-200 leu2-3, 2–112 lys2-801 trp1-1(am) ura3-52 bar1::HIS3] was used . YWO103 is a temperature sensitive mutant of S. cerevisiae containing mutant SUMO conjugating enzyme gene, Ubc9. YWO103 normally grows at 25°C but is unable to grow at restrictive temperature of 37°C. Transformation of strain YWO103 was carried out as described by Ito et al.,. Briefly, yeast cells were grown overnight in YPD medium (BD bioscience, USA) until reaching the mid-log phase (A600=1.0), and were then transformed with pVTL260-SaSce9 or empty pVTL260 (as control) plasmid by PEG/LiCl method. Transformants were selected in a minimal synthetic drop out medium lacking leucine (amino acid used as auxotrophic marker). Transformed yeast cells were checked by PCR for the presence of SaSce9 gene and colonies were then restreaked onto solid yeast peptone and dextrose (YPD) medium and incubated at permissive (25°C) and restrictive (37°C) temperatures. Cloning of genes was carried out using the protocols in laboratory manual . All the primers used in this study were designed using primer3 input version 4.0 .
RNA isolation and cDNA synthesis
Total RNA was isolated using the RNeasy plant midi kit (Qiagen, USA), and on-column DNAseI digestion was carried out to avoid the possible contamination of genomic DNA as per the manufacturer’s instruction (New England Biolab, USA). Quality of total RNA was checked in 1.2% formamide-denaturing agarose gel and quantification was carried out using ND-1000 spectrophotometer (Nanodrop Technologies, USA). First strand cDNA was synthesized using iScript™ first strand cDNA synthesis kit (Bio-Rad, USA) as per the instructions given in the manual.
Quantitative real time reverse transcription polymerase chain reaction (qRT-PCR)
Primers used for cloning and qRT-PCR of the SaSce9 gene
Stress related gene primers used for qRT-PCR in SaSce9 transgenic Arabidopsis plants
Generation of transgenic plants
The complete ORF of SaSce9 was amplified by PCR using forward primer SaSce9BglIIF and reverse primer SaSce9SpeIR (Table 1) containing the BglII and SpeI RE sites respectively, with Pfu DNA polymerase (NEB, USA). The identity and orientation of p35S-SaSce9 was further confirmed by DNA sequencing. The PCR product was digested with BglII and SpeI and cloned into pCAMBIA1304 vector (CAMBIA, Australia), as BglII-SpeI fragment of SaSce9 to generate the binary vector 35S-SaSce9. The construct harboring 35S-SaSce9, was introduced into Agrobacterium by freeze thaw method and transferred into wild type Columbia ecotype of Arabidopsis by floral dip method . Positive transgenic lines were screened on 40 mg/L hygromycin containing MS medium , and integration of transgene was confirmed by PCR using vector specific forward primer, pCAMF and SaSce9 specific reverse primer, SaSce9SpeIR (Table 2). Expression of SaSce9 transgene was verified by RT-PCR using cDNA made from total RNA isolated from positive SaSce9 transgenic plants. The SaSce9 transgenic plants of T3 generation were further used for salinity and drought stress experiments.
Salinity and drought tolerance assay
Seeds of WT and SaSce9 transgenic Arabidopsis were sterilized and directly sown on the vermiculite containing potting medium PM-15-13 (Lehle seeds, USA) and kept at 4°C for 4 days then transferred to growth chamber containing white fluorescent light of 100 μmol m-2 s-1 under 16 h light/8 h dark photoperiod at 23±1°C. Four week-old WT and transgenic plants were further supplied with 150 mM NaCl for 20 days for salinity stress, and water withheld for 14 days were used for drought test. Rosette leaves harvested at different time points were used for various physiological and biochemical assays. At least, three independent experiments with three replicates for each WT and, SaSce9 transgenic lines were studied.
Measurement of electrolyte leakage (EL), total chlorophyll content and proline content
Rosette leaves of four week old WT and SaSce9 transgenic Arabidopsis, grown under non-stress and stress conditions for one week, were harvested and used for physiological and biochemical measurements. For EL measurement, protocol of Bajji et al., was used. Briefly, 100 mg leaves were placed in 25 ml distilled water, shaken on a gyratory shaker (200 rpm) at room temperature for 2 h, and the initial conductivity (C1) was measured with a VWR® Traceable® Expanded Range Conductivity Meter (VWR, USA). The samples were then boiled for 10 min to induce maximum leakage. After cooling down at room temperature, electrolyte conductivity (C2) was measured and the relative electrical conductivity (C %) was calculated based on (C1/C2) × 100.
For estimation of total chlorophyll in WT and SaSce9 lines, protocol suggested by Arnon  was followed. About 100 mg of fine powder of leaf tissue was homogenized in 1 ml of 80% acetone and kept for 15 min at room temperature in dark. The crude extract was centrifuged for 20 min at 10000 rpm (rotation per minute) at room temperature, and the resultant supernatant was used for assessing absorbance at 663 and 645 nm with a spectrophotometer (Shimadzu UV-1600, Japan). Total chlorophyll content was computed in terms of fresh weight (FW).
For free proline estimation of WT and SaSce9 transgenic plants, standard protocol of Bates et al., was followed using fresh leaf tissues. Around 100 mg of tissues were used and extracted in 5 mL of 3% sulphosalicylic acid at 95°C for 15 min. After filtration, 2 mL of supernatant was transferred to a new tube containing 2 mL of acetic acid and 2 mL of acidified ninhydrin reagent. After 30 min of incubation at 95°C, samples were kept at room temperature for 30 min and 5 mL of toluene was added to the tube with shaking at 150 RPM, to extract red products. The absorbance of the toluene layer was determined at 532 nm using spectrophotometer (Shimadzu UV-1600, Japan). Standard curve prepared using different concentration of proline by same method was used for measuring free proline content in experimental samples. The experiment was repeated at least three times.
Na+ and K+estimation
Leaf tissues were harvested from unstressed, salt-stressed plants (three weeks old plants treated with 150 mM NaCl for 20 days) of WT and SaSce9 Arabidopsis, and oven-dried at 65°C for 48 h. Fifty milligrams of oven dried tissues were digested with 0.1% HNO3 at 100°C for 45 min and then Na+ and K+ concentrations were measured using inductively coupled plasma-mass spectrometry (ICP-MS, Perkin-Elmer Plasma 400 emission spectrometer).
In situ histochemical localization of O2-
For detection of superoxide radicals, histochemical staining with nitro blue tetrazolium (NBT) was followed according to Dong et al., with minor modification. Leaves detached from four week old WT and the SaSce9 Arabidopsis plants grown under non-stress or drought stress for next 7 days were vacuum-infiltrated in 1 mg/ml fresh NBT solution (prepared in 10 mM phosphate buffer, pH 7.8) and incubated at ambient temperature until appearance of dark spots. The stained leaves were then bleached in concentrated ethanol, kept in 70% ethanol, and photographed. Images were opened in Adobe Photoshop version 7 (Adobe Systems Incorporated, San Jose, CA) and stained areas of leaves were quantified as described by Lehr et al., .
Mean values, standard error, and t-test were performed with the help of pre-loaded software in Excel, available for statistical calculations (http://www.Physics.csbsju.edu/stats/t-test.html).
Reactive oxygen species
SUMO conjugating enzyme
Small Ubiquitin related Modifier
We are thankful to Dr. W. Seufert for supplying the temperature sensitive Ubc9 mutant yeast strain YWO103. The funding for this research was supported by United States Department of Agriculture-National Institute of Food and Agriculture. This manuscript is approved for publication by the Director of Louisiana Agricultural Experiment Station, USA as manuscript number 2012-306-7424.
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