1. Biochemistry and Chemical Biology
  2. Plant Biology
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Pyrophosphate modulates plant stress responses via SUMOylation

  1. M Görkem Patir-Nebioglu
  2. Zaida Andrés
  3. Melanie Krebs
  4. Fabian Fink
  5. Katarzyna Drzewicka
  6. Nicolas Stankovic-Valentin
  7. Shoji Segami
  8. Sebastian Schuck
  9. Michael Büttner
  10. Rüdiger Hell
  11. Masayoshi Maeshima
  12. Frauke Melchior
  13. Karin Schumacher  Is a corresponding author
  1. Heidelberg University, Germany
  2. Center for Molecular Biology of Heidelberg University (ZMBH) and DKFZ - ZMBH Alliance, Germany
  3. Nagoya University, Japan
Research Article
Cite this article as: eLife 2019;8:e44213 doi: 10.7554/eLife.44213
6 figures, 1 table and 2 additional files

Figures

Figure 1 with 3 supplements
PPi hydrolysis is required to rescue the freezing sensitive phenotype of fugu5-1.

(A) and (B) Freezing tolerance assay. Col-0, fugu5-1, UBQ:AVP1 and UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds were grown for 6 weeks at 22°C and were then moved to 4°C for cold-acclimation, or kept at 22°C for 4 days. Afterwards, plants were subjected to a 5 hr freezing temperature regime (0 to −10°C). After thawing at 4°C overnight, plants were moved back to 22°C. (A) Images were taken before cold-acclimation and one week after the freezing treatment. (B) Quantification of dead and alive leaves was done one week after the freezing treatment with n ≥ 75 leaves from 5 individual plants. 3 independent experiments were performed. Cold-acclimated UBQ:AVP1 and fugu5-1 are significantly different compared to the other genotypes (Student’s t-test p<0.05). (C) Electrolyte leakage assay of Col-0, fugu5-1, UBQ:AVP1 and UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds was performed on leaf material of acclimated and non-acclimated plants at indicated freezing temperatures. Error bars represent SD of the mean of n = 3 biological replicates. (D–G) Sugar and PPi measurements were done from extracts of acclimated (4°C) and non-acclimated (22°C) 6-week-old rosette leaves. Error bars show SD of the mean with n = 3 samples of one representative experiments. 3 biological replicates were performed. Significant differences are indicated by different letters (Two-way ANOVA followed by Tukey’s test, p<0.05).

https://doi.org/10.7554/eLife.44213.002
Figure 1—source data 1

(B) Survival of the 6 weeks old rosette leaves upon freezing.

(C) Electrolyte leakage analysis of the cold-acclimated and non-acclimated 6-weeks old rosette leaves upon exposure to freezing temperature. (D-G) Sugar and PPi measurements of the 6-weeks old rosette leaves.

https://doi.org/10.7554/eLife.44213.008
Figure 1—figure supplement 1
Increased Proton Transport Activity of V-ATPase upon Cold Acclimation Requires an Active V-PPase.

(A) Enriched tonoplast proteins were used to determine K+-stimulated PPi hydrolysis and H+ transport activity of V-PPase. (B) Enriched tonoplast proteins were used to determine KNO3-inhibited ATP hydrolysis and H+ transport activity of V-ATPase. (C) Cell sap pH measurement of rosette leaves. Error bars show SD of the mean with n = 12 samples of 3 biological replicates. (A–C) Col-0, fugu5-1 and UBQ:AVP1 were grown for 6 weeks under short-day conditions then were cold acclimated for 4 days at 4°C. Untreated plants were maintained in the same conditions as the growth period. Error bars represent SD of n = 3 biological replicates. Significant differences are indicated by different letters (Two-way ANOVA followed by Tukey’s test, p<0.05).

https://doi.org/10.7554/eLife.44213.003
Figure 1—figure supplement 1—source data 1

(A) V-PPase PPi hydrolysis and H+- transport measurements.

(B) V-ATPase ATP hydrolysis and H+-transport measurements. (C) Cell sap pH measurements.

https://doi.org/10.7554/eLife.44213.004
Figure 1—figure supplement 2
Overexpression of the Arabidopsis soluble pyrophosphatase PPa5 is sufficient to complement fugu5-1.

(A) Comparison of 6-week-old rosettes phenotypes of Col-0, fugu5-1 and overexpression lines of Arabidopsis vacuolar pyrophosphatase AVP1 and yeast soluble pyrophosphatase IPP1. (B) Representative images showing the localization of UBQ:PPa5-GFP to cytosol and nucleus in shoot (upper panel) and root cells (lower panel). Scale bars: 10 µm. (C) Cotyledon phenotypes of 5 days old seedlings of Col-0, fugu5-1 and UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds. (D) Comparison of 6-week-old short day grown rosette phenotypes of Col-0, fugu5-1 and UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds. (E) Measurements of fresh weight and whole rosette area of Col-0, fugu5-1 and UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds. Plants were grown for 6 weeks under short-day conditions. To determine rosette area Rosette Tracker plug-in of ImageJ is used. Error bars represent SD of the mean of n = 20 of 3 biological replicates. (F) Analysis of UBQ:PPa5-GFP protein amount in Col-0 and fugu5-1 background with anti-GFP. Soluble proteins from 6-week-old rosettes grown under short-day conditions were extracted. An internal control provided by SPL detection kit (DyeAGNOSTICS) was used for normalization. One representative image from three biological replicates is depicted. (G) Soluble proteins of Col-0, fugu5-1 and UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds were used to determine K+-stimulated PPi hydrolysis. Plants were grown for 6 weeks under short-day conditions. Error bars represent SD of n = 3 biological replicates. Significant differences are indicated by different letters (Two-way ANOVA followed by Tukey’s test, p<0.05).

https://doi.org/10.7554/eLife.44213.005
Figure 1—figure supplement 2—source data 1

(E) Fresh weight and area measurements of the 6-weeks old rosette leaves.

(G) Soluble pyrophosphatase activity measurements.

https://doi.org/10.7554/eLife.44213.006
Figure 1—figure supplement 3
Freezing tolerance phenotypes of the sPPase mutants.

(A) Wt, fugu5-1, ppa1, ppa1,4, ppa1,2,4,5 were grown for 6 weeks at 22°C and were then moved to 4°C for cold-acclimation, or kept at 22°C for 4 days. Electrolyte leakage was performed on leaf material of acclimated and non-acclimated plants at indicated temperatures. Error bars represent SD of the mean of n = 2 independent experiments.

https://doi.org/10.7554/eLife.44213.007
sPPase expression is induced upon cold exposure to control PPi that affects expression of CBFs and CBF target genes.

(A) qRT-PCR for the analysis of expression of PPa 1,2,4,5 and AVP1 in Col-0 and PPa 1,2,4 and 5 in fugu5-1. (B-C) Measurement of expression of CBF, COR and GolS3 genes in Col-0, fugu5-1 and UBQ:PPa5-GFP/fugu5-1 by qRT-PCR. (A-C) and () Plants were grown for six weeks under short-day conditions at 22°C. Afterwards, they were exposed to 4°C for indicated time periods. Whole rosettes were used for total RNA extraction. Actin2 expression was used for normalization. Error bars represent SD of the mean of n = 3 biological replicates. Data analysis was performed using the ΔΔCt method.

https://doi.org/10.7554/eLife.44213.009
Figure 2—source data 1

(A) Relative expression of the vacuolar and soluble pyrophosphatases in wt and the relative expression of the soluble pyrophosphtases in fugu5-1 exposed to 4°C for different hours.

(B-C) Relative expression of the cold regulated genes in wt, fugu5-1 and UBQ:PPa5-GFP/fugu5-1 upon exposure to 4°C for different hours.

https://doi.org/10.7554/eLife.44213.010
Figure 3 with 1 supplement
Modification of ICE1 and general SUMOylation upon cold exposure are inhibited in fugu5.

(A) Cold acclimation induces ICE1 SUMOylation which then activates CBFs and leads to the expression of downstream targets for the establishment of freezing tolerance. (B) Determination of the amount of ICE1 in Col-0, fugu5-1 and ice1-2 seedlings. Amount of TUBULIN was detected as loading control. Plants grown in long day conditions for 3 weeks. Black arrow indicates modified ICE1 dimer whereas red arrow indicates unmodified ICE1 dimer. (C) Comparison of the amount of the ICE1 under normal conditions (22°C) and after cold treatment (4°C, 3 hr) in Col-0 and fugu5-1 seedlings. 10-days-old liquid grown seedlings were used for total protein extraction. Anti-ICE1 was used as primary antibody. (D) Western blots comparing SUMOylation levels of Col-0 and fugu5-1 under normal conditions (22°C) and after cold treatment (4°C, 3 hr). (E) Western blots demonstrating the total SUMOylation in Col-0, fugu5-1, fugu5-3, UBQ:AVP1 and UBQ:PPa5-GFP under normal conditions (22°C) and after cold treatment (4°C, 3 hr). (D) and (E) 10 days old liquid grown seedlings were used for total protein extraction. Anti-SUMO1/2 was used as primary antibody. Whole lanes were measured for the calculation of protein amounts using ImageJ. cFBPase detection was used for normalization. Error bars represent SD of n ≥ 2 biological replicates. Asterisk indicates significant difference compared to Col-0 (Student’s t test; *p<0.05, ***p<0.001).

https://doi.org/10.7554/eLife.44213.011
Figure 3—source data 1

(D-E) Comparison of the amount of the total SUMOylation with and without cold treatment.

https://doi.org/10.7554/eLife.44213.013
Figure 3—figure supplement 1
Western blot detection of ICE1 in protein extracted in the presence of DTT.

(A) Comparison of total protein of 10-days-old Col-0 and fugu5-1 seedlings extracted ±DTT (5 mM) and NEM (20 mM).

https://doi.org/10.7554/eLife.44213.012
Heat shock-induced SUMOylation is also reduced in fugu5.

(A) Phenotypic analysis of 10-days-old Col-0, fugu5-1, UBQ:PPa5-GFP in Col-0 and fugu5-1 backgrounds and UBQ:AVP1 seedlings analysis before and after heat. Representative pictures of seedlings before and 4 days after completion of heat shock treatment (40°C, 4 hours) are depicted. (B) Seedling survival was determined 4 days after the heat shock. Alive and dead seedlings were counted and survival is shown as the percentage of the living seedlings. Error bars show SD of the mean with n ≥ 24 samples of one representative experiment. Two biological experiments were performed. Asterisk indicates significant difference compared to Col-0 (Student’s t test; **p<0.01, ***p<0.001). (C) SUMOylation levels of Col-0 and V-PPase mutant fugu5-1 were analysed with western blot under normal conditions (22°C) and after heat shock treatment (40°C, 30 min). (D) Measurement of the SUMO amount of Col-0, V-PPase mutants, UBQ:PPa5-GFP/fugu5-1 and UBQ:AVP1 seedlings after heat shock treatment (40°C, 30 min). (C) and (D) 10-days-old liquid grown seedlings are used for total protein extraction. Anti-SUMO1/2 (Agrisera) was used as primary antibody. Whole lanes were measured for the calculation of protein amounts using ImageJ. cFBPase detection was used for normalization. Error bars represent SD of n = 2 biological replicates. Asterisk indicates significant difference compared to Col-0 (Student’s t test; *p<0.05, **p<0.01, ***p<0.001).

https://doi.org/10.7554/eLife.44213.014
Figure 4—source data 1

(B) Survival measurement of the 10 days old seedlings upon heat shock.

(C-D) Comparison of the amount of the total SUMOylation with and without heat shock treatment.

https://doi.org/10.7554/eLife.44213.015
Increased PPi levels interfere with SUMOylation in yeast.

(A) Amount of the soluble pyrophosphatase protein in a conditional Ipp1 mutant of S. cerevisiae (GAL:HA-IPP1). Asterisk indicates significant difference compared to GAL:HA-IPP1 in galactose time point 0 hr (Student’s t test; ***p<0.001). Wt strain (W303) was used as a control. (B) Amount of total SUMOylation in W303 determined before and after heat stress. Asterisk indicates significant difference (Student’s t test; *p<0.05) (C) Measurement of total SUMO protein in conditional IPP1 mutant of S. cerevisiae (GAL:HA-IPP1). Asterisk indicates significant difference (Student’s t test; ***p<0.001). (A–C) Yeast is grown in synthetic complete medium supplemented with galactose at 28°C. After growing until OD600 0.5, part of the Ipp1 conditional mutant is switched to glucose supplemented medium to suppress the promoter and samples are collected at the indicated time points. For the heat treatment, cultures were switched to 40°C incubator for 1 hr. Error bars represent SD of n ≥ 2 biological replicates.

https://doi.org/10.7554/eLife.44213.016
Figure 5—source data 1

(A) Amount of IPP1 in different carbon supplies over time.

(B) Comparison of the total SUMOylation of wt yeast at 28 and 40°C. (C) Comparison of the total SUMOylation at 40°C, in Ipp1 conditional mutant.

https://doi.org/10.7554/eLife.44213.017
Figure 6 with 2 supplements
PPi regulates SUMOylation activity in vitro.

(A) Schematic illustration of the FRET-based sumoylation assays. Upon addition of ATP, the human SUMO E1 activating enzyme Aos1/Uba2 and the E2 conjugating enzyme Ubc9 form an isopeptide bond between the CFP-tagged human model substrate GAPtail and YFP-tagged mature SUMO. This can be detected via FRET measurements: Following the excitation of CFP, energy is transferred onto YFP. YFP and CFP emission are recorded upon excitation at 430 nm. Measurements are calculated as the ratio of the λem (YFP-SUMO 527 nm) to λex (CFP-RanGAPtail, 485 nm). (B) PPi titration showing that the increasing PPi concentration inhibits the SUMOylation activity. 1 mM ATP used for all the measurements. (C) In vitro SUMOylation assay showing that the E. coli soluble PPase is able to remove the inhibitory effect of PPi. After 10 min of measurement, one of the 8 µM PPi containing wells were supplied with 0.8 U of E.coli soluble PPase and control buffer was added to the rest of the wells. Measurements were continued for 20 more minutes. (D) PPi addition results in mixed inhibition of SUMOylation activity. Michaelis-Menten fittings of the measurements shown in Figure 6—figure supplement 1. Fittings are done in Origin software and Vmax and Km are calculated accordingly. (E) In vitro thioester bond formation assay showing Arabidopsis E1 (SAE2/SAE1a) and SUMO conjugation under different PPi concentrations. (B–D) Experiments were repeated four times, one representative experiment is shown.

https://doi.org/10.7554/eLife.44213.018
Figure 6—source data 1

(B) Ratio values (527/485 nm) of the FRET based SUMOylation showing the effect of the increasing amount of PPi concentrations.

(C) Ratio values (527/485 nm) of the FRET based SUMOylation assay showing that theE. colisoluble PPase is able to remove the inhibitory effect of PPi. (D) Calculation of the Vmax and Km of SUMOylation activity upon PPi inhibition based on the data shown in Figure 6—figure supplement 1.

https://doi.org/10.7554/eLife.44213.023
Figure 6—figure supplement 1
Elevated PPi concentrations leads to mixed inhibition of SUMOylation in vitro.

(A) SUMOylation assays demonstrating the effect of the increasing amounts of PPi to the speed of the reaction in a range of 0–10 µM ATP concentration. Experiments were repeated four times, one representative experiment is presented.

https://doi.org/10.7554/eLife.44213.019
Figure 6—figure supplement 1—source data 1

Ratio values (527/485 nm) of the FRET based SUMOylation assay showing the effect of the increasing amounts of PPto the speed of the reaction in a range of 0–10µMATP concentration.

https://doi.org/10.7554/eLife.44213.020
Figure 6—figure supplement 2
AtSAE1/2 purification and its activity in in vitro FRET based SUMOylation assay.

(A) Gel picture after purification of AtSAE1 and AtSAE2. Highlighted fractions from the final gel filtration step were combined, dialysed and used for subsequent experiments. (B) The purified Arabidopsis E1 activating enzyme is not functional in the FRET based SUMOylation assay. Assays were set up as described for Figure 6, but with recombinant Arabidopsis E1 enzyme. Human E1 activating enzyme was used in a positive control.

https://doi.org/10.7554/eLife.44213.021
Figure 6—figure supplement 2—source data 1

(A) Ratio values (527/485 nm) of the FRET-based SUMOylation assay with Arabidopsis E1.

https://doi.org/10.7554/eLife.44213.022

Tables

Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional
information
Gene
(Arabidopsis thaliana)
AtAVP1TAIR: AT1G15690
Gene
(Arabidopsis thaliana)
AtPPa1TAIR: AT1G01050
Gene
(Arabidopsis thaliana)
AtPPa2TAIR: AT2G18230
Gene
(Arabidopsis thaliana)
AtPPa4TAIR: AT3G53620
Gene
(Arabidopsis thaliana)
AtPPa5TAIR: AT4G01480
Gene
(Arabidopsis thaliana)
AtSUMO1TAIR: AT4G26840
Gene
(Arabidopsis thaliana)
AtICE1TAIR: AT3G26744
Gene
(Arabidopsis thaliana)
AtSAE1TAIR: AT4G24940
Gene
(Arabidopsis thaliana)
AtSAE2TAIR: AT2G21470
Gene
(Saccharomices
cerevisiae)
ScIPP1SGD: YBR011C
Strain, strain
background
(Agrobacterium
tumefaciens)
ASELampropoulos et al., 2013pSOUP+
Strain, strain
background
(Saccharomices
cerevisiae)
W303Szoradi et al., 2018SSY122
Strain, strain
background
(Saccharomices
cerevisiae)
IPP1prΔ::HIS3-
GAL1pr-HA-IPP1
this paperSSY2542Sebastian Schuck lab
Genetic reagent
(Arabidopsis thaliana)
fugu5-1Ferjani et al., 2011
Genetic reagent
(Arabidopsis thaliana)
fugu5-3Ferjani et al., 2011
Genetic reagent
(Arabidopsis thaliana)
ice1-2Nottingham Arabidopsis
Stock Centre (NASC)
SALK_003155
Genetic reagent
(Arabidopsis thaliana)
ppa1Segami et al., 2018; NASCSAIL_251_D07
Genetic reagent
(Arabidopsis thaliana)
ppa1,4this paperSAIL_251_D07, SAIL_916_C08Cross between the mutants
ppa1 and ppa4 described
in Segami et al., 2018
Masayoshi Maeshima lab
Genetic reagent
(Arabidopsis thaliana)
ppa1,2,4,5Segami et al., 2018SAIL_251_D07,
SAIL_618_H05,
SAIL_916_C08,
SALK_014647
Biological sample
(Arabidopsis thaliana)
AVP1:IPP1/fugu5-1Ferjani et al., 2011AVP1 promoter:IPP1
coding sequence;
fugu5-1 mutant background
Biological sample
(Arabidopsis thaliana)
UBQ:AVP1 #18–4Kriegel et al., 2015UBQ promoter:AVP1
coding sequence;
Col-0 wild-type background
Biological sample
(Arabidopsis thaliana)
UBQ:PPa5-GFP/Col-0this paper,UBQ promoter:PPa5-GFP
coding sequence;
Col-0 wild-type background.
Karin Schumacher lab
Biological sample
(Arabidopsis thaliana)
UBQ:PPa5-GFP/fugu5-1this paper,UBQ promoter:PPa5-GFP
coding sequence;
fugu5-1 wild-type
background. Karin
Schumacher lab
AntibodyAnti-SUMO1
(rabbit polyclonal)
AgriseraAS08308(1:1000)
AntibodyAnti-ICE1
(rabbit polyclonal)
AgriseraAS163971(1:1000)
AntibodyAnti-cFBPase
(rabbit polyclonal)
AgriseraAS04043(1:5000)
AntibodyAnti-rabbit-HRP
(Goat polyclonal)
PromegaW401B(1:10000)
AntibodyAnti-IPP1
(rabbit polyclonal)
Antibodies-
online GmbH
ABIN459215(1:1000)
AntibodyAnti-PGK1
(mouse monoclonal)
AbcamAB113687(1:100000)
AntibodyAnti-mouse-HRP
(sheep polyclonal)
GE Healthcare UKNXA931(1:5000)
AntibodyAnti-V-PPase
(rabbit polyclonal)
AgriseraAS121849(1:10000)
AntibodyAnti-VHA-C
(rabbit polyclonal)
Karin Schumacher labSchumacher et al., 1999(1:2000)
AntibodyAnti-GFP
(rabbit polyclonal)
Karin Schumacher labRoth et al., 2018(1:10000)
Recombinant
DNA reagent
UBQ:PPa5-GFPthis paper,vector-promoter:tagged-protein construct. Karin
Schumacher lab
Recombinant
DNA reagent
pET28b(+)−6xHIS
-AtSUMO1(1–93)
this paper,vector-tagged-protein
construct. Karin
Schumacher lab
Recombinant
DNA reagent
pET28-6xHIS-AtSAE1this paper,vector-tagged-protein
construct. Frauke Melchior lab
Recombinant
DNA reagent
pET11d-AtSAE2this papervector-protein construct.
Frauke Melchior lab
Recombinant
DNA reagent
pFA6a-His3M × 6-
PGAL1
this paper,vector-promoter:tagged-protein construct. Sebastian Schuck lab
Peptide,
recombinant
protein
CFP-RanGAPtailBossis et al., 2005;
Werner et al., 2009
Peptide,
recombinant
protein
YFP-SUMOBossis et al., 2005;
Werner et al., 2009
Peptide,
recombinant
protein
Uba2/Aos1Bossis et al., 2005;
Werner et al., 2009
Peptide,
recombinant
protein
Ubc9Bossis et al., 2005;
Werner et al., 2009
Peptide,
recombinant
protein
6xHis-AtSUMO1this paperFor in vitro thioester
bond formation assays
Peptide,
recombinant
protein
AtSAE1this paperFor in vitro thioester
bond formation assays
Peptide,
recombinant
protein
AtSAE2this paperFor in vitro thioester
bond formation assays
Commercial
assay or kit
SPL kitNH DyeAgnosticsWestern blot protein
quantification kit

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided.

Additional files

Supplementary file 1

Additional resources.

(A) Primers of UBQ:PPa5-GFP construct. (B) List of GG modules. (C) qRT primers. (D) Primers for constructs used in protein purification. (E) Statistical analysis (One-way ANOVA followed by Tukey’s test, p<0.05) of the electrolyte leakage assay (Figure 1C). Significant values are highlighted.

https://doi.org/10.7554/eLife.44213.024
Transparent reporting form
https://doi.org/10.7554/eLife.44213.025

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